partition stringclasses 3
values | func_name stringlengths 1 134 | docstring stringlengths 1 46.9k | path stringlengths 4 223 | original_string stringlengths 75 104k | code stringlengths 75 104k | docstring_tokens listlengths 1 1.97k | repo stringlengths 7 55 | language stringclasses 1
value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
|---|---|---|---|---|---|---|---|---|---|---|---|
test | sv_variant | Display a specific structural variant. | scout/server/blueprints/variants/views.py | def sv_variant(institute_id, case_name, variant_id):
"""Display a specific structural variant."""
data = controllers.sv_variant(store, institute_id, case_name, variant_id)
return data | def sv_variant(institute_id, case_name, variant_id):
"""Display a specific structural variant."""
data = controllers.sv_variant(store, institute_id, case_name, variant_id)
return data | [
"Display",
"a",
"specific",
"structural",
"variant",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/views.py#L299-L302 | [
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test | str_variant | Display a specific STR variant. | scout/server/blueprints/variants/views.py | def str_variant(institute_id, case_name, variant_id):
"""Display a specific STR variant."""
data = controllers.str_variant(store, institute_id, case_name, variant_id)
return data | def str_variant(institute_id, case_name, variant_id):
"""Display a specific STR variant."""
data = controllers.str_variant(store, institute_id, case_name, variant_id)
return data | [
"Display",
"a",
"specific",
"STR",
"variant",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/views.py#L306-L309 | [
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] | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | variant_update | Update user-defined information about a variant: manual rank & ACMG. | scout/server/blueprints/variants/views.py | def variant_update(institute_id, case_name, variant_id):
"""Update user-defined information about a variant: manual rank & ACMG."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = re... | def variant_update(institute_id, case_name, variant_id):
"""Update user-defined information about a variant: manual rank & ACMG."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = re... | [
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"user",
"-",
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"information",
"about",
"a",
"variant",
":",
"manual",
"rank",
"&",
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"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/views.py#L312-L364 | [
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test | verify | Start procedure to validate variant using other techniques. | scout/server/blueprints/variants/views.py | def verify(institute_id, case_name, variant_id, variant_category, order):
"""Start procedure to validate variant using other techniques."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
... | def verify(institute_id, case_name, variant_id, variant_category, order):
"""Start procedure to validate variant using other techniques."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
... | [
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test | clinvar | Build a clinVar submission form for a variant. | scout/server/blueprints/variants/views.py | def clinvar(institute_id, case_name, variant_id):
"""Build a clinVar submission form for a variant."""
data = controllers.clinvar_export(store, institute_id, case_name, variant_id)
if request.method == 'GET':
return data
else: #POST
form_dict = request.form.to_dict()
submission_o... | def clinvar(institute_id, case_name, variant_id):
"""Build a clinVar submission form for a variant."""
data = controllers.clinvar_export(store, institute_id, case_name, variant_id)
if request.method == 'GET':
return data
else: #POST
form_dict = request.form.to_dict()
submission_o... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/views.py#L387-L402 | [
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"'GET'... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | cancer_variants | Show cancer variants overview. | scout/server/blueprints/variants/views.py | def cancer_variants(institute_id, case_name):
"""Show cancer variants overview."""
data = controllers.cancer_variants(store, request.args, institute_id, case_name)
return data | def cancer_variants(institute_id, case_name):
"""Show cancer variants overview."""
data = controllers.cancer_variants(store, request.args, institute_id, case_name)
return data | [
"Show",
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test | variant_acmg | ACMG classification form. | scout/server/blueprints/variants/views.py | def variant_acmg(institute_id, case_name, variant_id):
"""ACMG classification form."""
if request.method == 'GET':
data = controllers.variant_acmg(store, institute_id, case_name, variant_id)
return data
else:
criteria = []
criteria_terms = request.form.getlist('criteria')
... | def variant_acmg(institute_id, case_name, variant_id):
"""ACMG classification form."""
if request.method == 'GET':
data = controllers.variant_acmg(store, institute_id, case_name, variant_id)
return data
else:
criteria = []
criteria_terms = request.form.getlist('criteria')
... | [
"ACMG",
"classification",
"form",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/views.py#L415-L433 | [
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"variant... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | evaluation | Show or delete an ACMG evaluation. | scout/server/blueprints/variants/views.py | def evaluation(evaluation_id):
"""Show or delete an ACMG evaluation."""
evaluation_obj = store.get_evaluation(evaluation_id)
controllers.evaluation(store, evaluation_obj)
if request.method == 'POST':
link = url_for('.variant', institute_id=evaluation_obj['institute']['_id'],
... | def evaluation(evaluation_id):
"""Show or delete an ACMG evaluation."""
evaluation_obj = store.get_evaluation(evaluation_id)
controllers.evaluation(store, evaluation_obj)
if request.method == 'POST':
link = url_for('.variant', institute_id=evaluation_obj['institute']['_id'],
... | [
"Show",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/views.py#L438-L450 | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | acmg | Calculate an ACMG classification from submitted criteria. | scout/server/blueprints/variants/views.py | def acmg():
"""Calculate an ACMG classification from submitted criteria."""
criteria = request.args.getlist('criterion')
classification = get_acmg(criteria)
return jsonify(dict(classification=classification)) | def acmg():
"""Calculate an ACMG classification from submitted criteria."""
criteria = request.args.getlist('criterion')
classification = get_acmg(criteria)
return jsonify(dict(classification=classification)) | [
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")... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | upload_panel | Parse gene panel file and fill in HGNC symbols for filter. | scout/server/blueprints/variants/views.py | def upload_panel(institute_id, case_name):
"""Parse gene panel file and fill in HGNC symbols for filter."""
file = form.symbol_file.data
if file.filename == '':
flash('No selected file', 'warning')
return redirect(request.referrer)
try:
stream = io.StringIO(file.stream.read().d... | def upload_panel(institute_id, case_name):
"""Parse gene panel file and fill in HGNC symbols for filter."""
file = form.symbol_file.data
if file.filename == '':
flash('No selected file', 'warning')
return redirect(request.referrer)
try:
stream = io.StringIO(file.stream.read().d... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/views.py#L463-L496 | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | download_verified | Download all verified variants for user's cases | scout/server/blueprints/variants/views.py | def download_verified():
"""Download all verified variants for user's cases"""
user_obj = store.user(current_user.email)
user_institutes = user_obj.get('institutes')
temp_excel_dir = os.path.join(variants_bp.static_folder, 'verified_folder')
os.makedirs(temp_excel_dir, exist_ok=True)
written_fi... | def download_verified():
"""Download all verified variants for user's cases"""
user_obj = store.user(current_user.email)
user_institutes = user_obj.get('institutes')
temp_excel_dir = os.path.join(variants_bp.static_folder, 'verified_folder')
os.makedirs(temp_excel_dir, exist_ok=True)
written_fi... | [
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"all",
"verified",
"variants",
"for",
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"s",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/views.py#L500-L529 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | genes_by_alias | Return a dictionary with hgnc symbols as keys
Value of the dictionaries are information about the hgnc ids for a symbol.
If the symbol is primary for a gene then 'true_id' will exist.
A list of hgnc ids that the symbol points to is in ids.
Args:
hgnc_genes(dict): a dictionary with hgnc_id as k... | scout/utils/link.py | def genes_by_alias(hgnc_genes):
"""Return a dictionary with hgnc symbols as keys
Value of the dictionaries are information about the hgnc ids for a symbol.
If the symbol is primary for a gene then 'true_id' will exist.
A list of hgnc ids that the symbol points to is in ids.
Args:
hgnc_gene... | def genes_by_alias(hgnc_genes):
"""Return a dictionary with hgnc symbols as keys
Value of the dictionaries are information about the hgnc ids for a symbol.
If the symbol is primary for a gene then 'true_id' will exist.
A list of hgnc ids that the symbol points to is in ids.
Args:
hgnc_gene... | [
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"symbols",
"as",
"keys"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/utils/link.py#L18-L57 | [
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"]",... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | add_ensembl_info | Add the coordinates from ensembl
Args:
genes(dict): Dictionary with all genes
ensembl_lines(iteable): Iteable with raw ensembl info | scout/utils/link.py | def add_ensembl_info(genes, ensembl_lines):
"""Add the coordinates from ensembl
Args:
genes(dict): Dictionary with all genes
ensembl_lines(iteable): Iteable with raw ensembl info
"""
LOG.info("Adding ensembl coordinates")
# Parse and add the ensembl gene info
if isinsta... | def add_ensembl_info(genes, ensembl_lines):
"""Add the coordinates from ensembl
Args:
genes(dict): Dictionary with all genes
ensembl_lines(iteable): Iteable with raw ensembl info
"""
LOG.info("Adding ensembl coordinates")
# Parse and add the ensembl gene info
if isinsta... | [
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test | add_exac_info | Add information from the exac genes
Currently we only add the pLi score on gene level
The exac resource only use HGNC symbol to identify genes so we need
our alias mapping.
Args:
genes(dict): Dictionary with all genes
alias_genes(dict): Genes mapped to all aliases
... | scout/utils/link.py | def add_exac_info(genes, alias_genes, exac_lines):
"""Add information from the exac genes
Currently we only add the pLi score on gene level
The exac resource only use HGNC symbol to identify genes so we need
our alias mapping.
Args:
genes(dict): Dictionary with all genes
... | def add_exac_info(genes, alias_genes, exac_lines):
"""Add information from the exac genes
Currently we only add the pLi score on gene level
The exac resource only use HGNC symbol to identify genes so we need
our alias mapping.
Args:
genes(dict): Dictionary with all genes
... | [
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test | add_omim_info | Add omim information
We collect information on what phenotypes that are associated with a gene,
what inheritance models that are associated and the correct omim id.
Args:
genes(dict): Dictionary with all genes
alias_genes(dict): Genes mapped to all aliases
genemap_lines(ite... | scout/utils/link.py | def add_omim_info(genes, alias_genes, genemap_lines, mim2gene_lines):
"""Add omim information
We collect information on what phenotypes that are associated with a gene,
what inheritance models that are associated and the correct omim id.
Args:
genes(dict): Dictionary with all genes
... | def add_omim_info(genes, alias_genes, genemap_lines, mim2gene_lines):
"""Add omim information
We collect information on what phenotypes that are associated with a gene,
what inheritance models that are associated and the correct omim id.
Args:
genes(dict): Dictionary with all genes
... | [
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"hgnc... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | add_incomplete_penetrance | Add information of incomplete penetrance | scout/utils/link.py | def add_incomplete_penetrance(genes, alias_genes, hpo_lines):
"""Add information of incomplete penetrance"""
LOG.info("Add incomplete penetrance info")
for hgnc_symbol in get_incomplete_penetrance_genes(hpo_lines):
for hgnc_id in get_correct_ids(hgnc_symbol, alias_genes):
genes[hgnc_id][... | def add_incomplete_penetrance(genes, alias_genes, hpo_lines):
"""Add information of incomplete penetrance"""
LOG.info("Add incomplete penetrance info")
for hgnc_symbol in get_incomplete_penetrance_genes(hpo_lines):
for hgnc_id in get_correct_ids(hgnc_symbol, alias_genes):
genes[hgnc_id][... | [
"Add",
"information",
"of",
"incomplete",
"penetrance"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/utils/link.py#L136-L141 | [
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"h... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | get_correct_ids | Try to get the correct gene based on hgnc_symbol
The HGNC symbol is unfortunately not a persistent gene identifier.
Many of the resources that are used by Scout only provides the hgnc symbol to
identify a gene. We need a way to guess what gene is pointed at.
Args:
hgnc_symbol(str): Th... | scout/utils/link.py | def get_correct_ids(hgnc_symbol, alias_genes):
"""Try to get the correct gene based on hgnc_symbol
The HGNC symbol is unfortunately not a persistent gene identifier.
Many of the resources that are used by Scout only provides the hgnc symbol to
identify a gene. We need a way to guess what gene is p... | def get_correct_ids(hgnc_symbol, alias_genes):
"""Try to get the correct gene based on hgnc_symbol
The HGNC symbol is unfortunately not a persistent gene identifier.
Many of the resources that are used by Scout only provides the hgnc symbol to
identify a gene. We need a way to guess what gene is p... | [
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... | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/utils/link.py#L144-L167 | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | link_genes | Gather information from different sources and return a gene dict
Extract information collected from a number of sources and combine them
into a gene dict with HGNC symbols as keys.
hgnc_id works as the primary symbol and it is from this source we gather
as much information as possible (hgnc_complete_s... | scout/utils/link.py | def link_genes(ensembl_lines, hgnc_lines, exac_lines, mim2gene_lines,
genemap_lines, hpo_lines):
"""Gather information from different sources and return a gene dict
Extract information collected from a number of sources and combine them
into a gene dict with HGNC symbols as keys.
hgnc_i... | def link_genes(ensembl_lines, hgnc_lines, exac_lines, mim2gene_lines,
genemap_lines, hpo_lines):
"""Gather information from different sources and return a gene dict
Extract information collected from a number of sources and combine them
into a gene dict with HGNC symbols as keys.
hgnc_i... | [
"Gather",
"information",
"from",
"different",
"sources",
"and",
"return",
"a",
"gene",
"dict"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/utils/link.py#L169-L215 | [
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"(",
"\"Linking genes\"",
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"# HGNC genes are the main source, ... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | matchmaker_request | Send a request to MatchMaker and return its response
Args:
url(str): url to send request to
token(str): MME server authorization token
method(str): 'GET', 'POST' or 'DELETE'
content_type(str): MME request Content-Type
accept(str): accepted response
data(dict): eventu... | scout/utils/matchmaker.py | def matchmaker_request(url, token, method, content_type=None, accept=None, data=None):
"""Send a request to MatchMaker and return its response
Args:
url(str): url to send request to
token(str): MME server authorization token
method(str): 'GET', 'POST' or 'DELETE'
content_type(st... | def matchmaker_request(url, token, method, content_type=None, accept=None, data=None):
"""Send a request to MatchMaker and return its response
Args:
url(str): url to send request to
token(str): MME server authorization token
method(str): 'GET', 'POST' or 'DELETE'
content_type(st... | [
"Send",
"a",
"request",
"to",
"MatchMaker",
"and",
"return",
"its",
"response"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/utils/matchmaker.py#L10-L58 | [
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"to... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | mme_nodes | Return the available MatchMaker nodes
Args:
mme_base_url(str): base URL of MME service
token(str): MME server authorization token
Returns:
nodes(list): a list of node disctionaries | scout/utils/matchmaker.py | def mme_nodes(mme_base_url, token):
"""Return the available MatchMaker nodes
Args:
mme_base_url(str): base URL of MME service
token(str): MME server authorization token
Returns:
nodes(list): a list of node disctionaries
"""
nodes = []
if not mme_base_url or not token:
... | def mme_nodes(mme_base_url, token):
"""Return the available MatchMaker nodes
Args:
mme_base_url(str): base URL of MME service
token(str): MME server authorization token
Returns:
nodes(list): a list of node disctionaries
"""
nodes = []
if not mme_base_url or not token:
... | [
"Return",
"the",
"available",
"MatchMaker",
"nodes"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/utils/matchmaker.py#L61-L77 | [
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"n... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | get_cytoband_coordinates | Get the cytoband coordinate for a position
Args:
chrom(str)
pos(int)
Returns:
coordinate(str) | scout/parse/variant/coordinates.py | def get_cytoband_coordinates(chrom, pos):
"""Get the cytoband coordinate for a position
Args:
chrom(str)
pos(int)
Returns:
coordinate(str)
"""
coordinate = ""
if chrom in CYTOBANDS:
for interval in CYTOBANDS[chrom][pos]:
coordinate = interval.data
... | def get_cytoband_coordinates(chrom, pos):
"""Get the cytoband coordinate for a position
Args:
chrom(str)
pos(int)
Returns:
coordinate(str)
"""
coordinate = ""
if chrom in CYTOBANDS:
for interval in CYTOBANDS[chrom][pos]:
coordinate = interval.data
... | [
"Get",
"the",
"cytoband",
"coordinate",
"for",
"a",
"position"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/variant/coordinates.py#L3-L19 | [
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"coordinate",
"=",
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".",
"d... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | get_sub_category | Get the subcategory for a VCF variant
The sub categories are:
'snv', 'indel', 'del', 'ins', 'dup', 'bnd', 'inv'
Args:
alt_len(int)
ref_len(int)
category(str)
svtype(str)
Returns:
subcategory(str) | scout/parse/variant/coordinates.py | def get_sub_category(alt_len, ref_len, category, svtype=None):
"""Get the subcategory for a VCF variant
The sub categories are:
'snv', 'indel', 'del', 'ins', 'dup', 'bnd', 'inv'
Args:
alt_len(int)
ref_len(int)
category(str)
svtype(str)
Returns:
subcateg... | def get_sub_category(alt_len, ref_len, category, svtype=None):
"""Get the subcategory for a VCF variant
The sub categories are:
'snv', 'indel', 'del', 'ins', 'dup', 'bnd', 'inv'
Args:
alt_len(int)
ref_len(int)
category(str)
svtype(str)
Returns:
subcateg... | [
"Get",
"the",
"subcategory",
"for",
"a",
"VCF",
"variant"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/variant/coordinates.py#L21-L46 | [
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"alt_len",... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | get_length | Return the length of a variant
Args:
alt_len(int)
ref_len(int)
category(str)
svtype(str)
svlen(int) | scout/parse/variant/coordinates.py | def get_length(alt_len, ref_len, category, pos, end, svtype=None, svlen=None):
"""Return the length of a variant
Args:
alt_len(int)
ref_len(int)
category(str)
svtype(str)
svlen(int)
"""
# -1 would indicate uncertain length
length = -1
if category in ('snv... | def get_length(alt_len, ref_len, category, pos, end, svtype=None, svlen=None):
"""Return the length of a variant
Args:
alt_len(int)
ref_len(int)
category(str)
svtype(str)
svlen(int)
"""
# -1 would indicate uncertain length
length = -1
if category in ('snv... | [
"Return",
"the",
"length",
"of",
"a",
"variant"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/variant/coordinates.py#L48-L76 | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | get_end | Return the end coordinate for a variant
Args:
pos(int)
alt(str)
category(str)
snvend(str)
svend(int)
svlen(int)
Returns:
end(int) | scout/parse/variant/coordinates.py | def get_end(pos, alt, category, snvend=None, svend=None, svlen=None):
"""Return the end coordinate for a variant
Args:
pos(int)
alt(str)
category(str)
snvend(str)
svend(int)
svlen(int)
Returns:
end(int)
"""
# If nothing is known we set end to... | def get_end(pos, alt, category, snvend=None, svend=None, svlen=None):
"""Return the end coordinate for a variant
Args:
pos(int)
alt(str)
category(str)
snvend(str)
svend(int)
svlen(int)
Returns:
end(int)
"""
# If nothing is known we set end to... | [
"Return",
"the",
"end",
"coordinate",
"for",
"a",
"variant"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/variant/coordinates.py#L78-L115 | [
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"# If variant is snv or indel we know ... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_coordinates | Find out the coordinates for a variant
Args:
variant(cyvcf2.Variant)
Returns:
coordinates(dict): A dictionary on the form:
{
'position':<int>,
'end':<int>,
'end_chrom':<str>,
'length':<int>,
'sub_category':<str>,
'... | scout/parse/variant/coordinates.py | def parse_coordinates(variant, category):
"""Find out the coordinates for a variant
Args:
variant(cyvcf2.Variant)
Returns:
coordinates(dict): A dictionary on the form:
{
'position':<int>,
'end':<int>,
'end_chrom':<str>,
'length':<int>... | def parse_coordinates(variant, category):
"""Find out the coordinates for a variant
Args:
variant(cyvcf2.Variant)
Returns:
coordinates(dict): A dictionary on the form:
{
'position':<int>,
'end':<int>,
'end_chrom':<str>,
'length':<int>... | [
"Find",
"out",
"the",
"coordinates",
"for",
"a",
"variant"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/variant/coordinates.py#L117-L192 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_cytoband | Parse iterable with cytoband coordinates
Args:
lines(iterable): Strings on format "chr1\t2300000\t5400000\tp36.32\tgpos25"
Returns:
cytobands(dict): Dictionary with chromosome names as keys and
interval trees as values | scout/parse/cytoband.py | def parse_cytoband(lines):
"""Parse iterable with cytoband coordinates
Args:
lines(iterable): Strings on format "chr1\t2300000\t5400000\tp36.32\tgpos25"
Returns:
cytobands(dict): Dictionary with chromosome names as keys and
interval trees as values
... | def parse_cytoband(lines):
"""Parse iterable with cytoband coordinates
Args:
lines(iterable): Strings on format "chr1\t2300000\t5400000\tp36.32\tgpos25"
Returns:
cytobands(dict): Dictionary with chromosome names as keys and
interval trees as values
... | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | cli | docstring for cli | scout/parse/cytoband.py | def cli(infile):
"""docstring for cli"""
lines = get_file_handle(infile)
cytobands = parse_cytoband(lines)
print("Check some coordinates:")
print("checking chrom 1 pos 2")
intervals = cytobands['1'][2]
for interval in intervals:
print(interval)
print(interval.begin)... | def cli(infile):
"""docstring for cli"""
lines = get_file_handle(infile)
cytobands = parse_cytoband(lines)
print("Check some coordinates:")
print("checking chrom 1 pos 2")
intervals = cytobands['1'][2]
for interval in intervals:
print(interval)
print(interval.begin)... | [
"docstring",
"for",
"cli"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/cytoband.py#L44-L65 | [
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"="... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | update_panel | Update a gene panel in the database
We need to update the actual gene panel and then all cases that refers to the panel.
Args:
adapter(scout.adapter.MongoAdapter)
panel_name(str): Unique name for a gene panel
panel_version(float)
new_version(float)
new_date(date... | scout/update/panel.py | def update_panel(adapter, panel_name, panel_version, new_version=None, new_date=None):
"""Update a gene panel in the database
We need to update the actual gene panel and then all cases that refers to the panel.
Args:
adapter(scout.adapter.MongoAdapter)
panel_name(str): Unique name ... | def update_panel(adapter, panel_name, panel_version, new_version=None, new_date=None):
"""Update a gene panel in the database
We need to update the actual gene panel and then all cases that refers to the panel.
Args:
adapter(scout.adapter.MongoAdapter)
panel_name(str): Unique name ... | [
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test | cli | scout: manage interactions with a scout instance. | scout/commands/base.py | def cli(context, mongodb, username, password, authdb, host, port, loglevel, config, demo):
"""scout: manage interactions with a scout instance."""
# log_format = "%(message)s" if sys.stdout.isatty() else None
log_format = None
coloredlogs.install(level=loglevel, fmt=log_format)
LOG.info("Running sco... | def cli(context, mongodb, username, password, authdb, host, port, loglevel, config, demo):
"""scout: manage interactions with a scout instance."""
# log_format = "%(message)s" if sys.stdout.isatty() else None
log_format = None
coloredlogs.install(level=loglevel, fmt=log_format)
LOG.info("Running sco... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/base.py#L57-L111 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_exac_line | Parse an exac formated line
Args:
line(list): A list with exac gene info
header(list): A list with the header info
Returns:
exac_info(dict): A dictionary with the relevant info | scout/parse/exac.py | def parse_exac_line(line, header):
"""Parse an exac formated line
Args:
line(list): A list with exac gene info
header(list): A list with the header info
Returns:
exac_info(dict): A dictionary with the relevant info
"""
exac_gene = {}
spli... | def parse_exac_line(line, header):
"""Parse an exac formated line
Args:
line(list): A list with exac gene info
header(list): A list with the header info
Returns:
exac_info(dict): A dictionary with the relevant info
"""
exac_gene = {}
spli... | [
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"splitted_line... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_exac_genes | Parse lines with exac formated genes
This is designed to take a dump with genes from exac.
This is downloaded from:
ftp.broadinstitute.org/pub/ExAC_release//release0.3/functional_gene_constraint/
fordist_cleaned_exac_r03_march16_z_pli_rec_null_data.txt
Args... | scout/parse/exac.py | def parse_exac_genes(lines):
"""Parse lines with exac formated genes
This is designed to take a dump with genes from exac.
This is downloaded from:
ftp.broadinstitute.org/pub/ExAC_release//release0.3/functional_gene_constraint/
fordist_cleaned_exac_r03_march16_z_pli... | def parse_exac_genes(lines):
"""Parse lines with exac formated genes
This is designed to take a dump with genes from exac.
This is downloaded from:
ftp.broadinstitute.org/pub/ExAC_release//release0.3/functional_gene_constraint/
fordist_cleaned_exac_r03_march16_z_pli... | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | panels | Show all panels for a case. | scout/server/blueprints/panels/views.py | def panels():
"""Show all panels for a case."""
if request.method == 'POST':
# update an existing panel
csv_file = request.files['csv_file']
content = csv_file.stream.read()
lines = None
try:
if b'\n' in content:
lines = content.decode('utf-8',... | def panels():
"""Show all panels for a case."""
if request.method == 'POST':
# update an existing panel
csv_file = request.files['csv_file']
content = csv_file.stream.read()
lines = None
try:
if b'\n' in content:
lines = content.decode('utf-8',... | [
"Show",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/panels/views.py#L20-L81 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | panel | Display (and add pending updates to) a specific gene panel. | scout/server/blueprints/panels/views.py | def panel(panel_id):
"""Display (and add pending updates to) a specific gene panel."""
panel_obj = store.gene_panel(panel_id) or store.panel(panel_id)
if request.method == 'POST':
raw_hgnc_id = request.form['hgnc_id']
if '|' in raw_hgnc_id:
raw_hgnc_id = raw_hgnc_id.split(' | ', ... | def panel(panel_id):
"""Display (and add pending updates to) a specific gene panel."""
panel_obj = store.gene_panel(panel_id) or store.panel(panel_id)
if request.method == 'POST':
raw_hgnc_id = request.form['hgnc_id']
if '|' in raw_hgnc_id:
raw_hgnc_id = raw_hgnc_id.split(' | ', ... | [
"Display",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/panels/views.py#L86-L123 | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | panel_update | Update panel to a new version. | scout/server/blueprints/panels/views.py | def panel_update(panel_id):
"""Update panel to a new version."""
panel_obj = store.panel(panel_id)
update_version = request.form.get('version', None)
new_panel_id = store.apply_pending(panel_obj, update_version)
return redirect(url_for('panels.panel', panel_id=new_panel_id)) | def panel_update(panel_id):
"""Update panel to a new version."""
panel_obj = store.panel(panel_id)
update_version = request.form.get('version', None)
new_panel_id = store.apply_pending(panel_obj, update_version)
return redirect(url_for('panels.panel', panel_id=new_panel_id)) | [
"Update",
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"a",
"new",
"version",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/panels/views.py#L127-L132 | [
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test | panel_export | Export panel to PDF file | scout/server/blueprints/panels/views.py | def panel_export(panel_id):
"""Export panel to PDF file"""
panel_obj = store.panel(panel_id)
data = controllers.panel_export(store, panel_obj)
data['report_created_at'] = datetime.datetime.now().strftime("%Y-%m-%d")
html_report = render_template('panels/panel_pdf_simple.html', **data)
return ren... | def panel_export(panel_id):
"""Export panel to PDF file"""
panel_obj = store.panel(panel_id)
data = controllers.panel_export(store, panel_obj)
data['report_created_at'] = datetime.datetime.now().strftime("%Y-%m-%d")
html_report = render_template('panels/panel_pdf_simple.html', **data)
return ren... | [
"Export",
"panel",
"to",
"PDF",
"file"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/panels/views.py#L136-L142 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | gene_edit | Edit additional information about a panel gene. | scout/server/blueprints/panels/views.py | def gene_edit(panel_id, hgnc_id):
"""Edit additional information about a panel gene."""
panel_obj = store.panel(panel_id)
hgnc_gene = store.hgnc_gene(hgnc_id)
panel_gene = controllers.existing_gene(store, panel_obj, hgnc_id)
form = PanelGeneForm()
transcript_choices = []
for transcript in h... | def gene_edit(panel_id, hgnc_id):
"""Edit additional information about a panel gene."""
panel_obj = store.panel(panel_id)
hgnc_gene = store.hgnc_gene(hgnc_id)
panel_gene = controllers.existing_gene(store, panel_obj, hgnc_id)
form = PanelGeneForm()
transcript_choices = []
for transcript in h... | [
"Edit",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/panels/views.py#L147-L177 | [
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"st... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | delivery_report | Add delivery report to an existing case. | scout/commands/load/report.py | def delivery_report(context, case_id, report_path,
update):
"""Add delivery report to an existing case."""
adapter = context.obj['adapter']
try:
load_delivery_report(adapter=adapter, case_id=case_id,
report_path=report_path, update=update)
L... | def delivery_report(context, case_id, report_path,
update):
"""Add delivery report to an existing case."""
adapter = context.obj['adapter']
try:
load_delivery_report(adapter=adapter, case_id=case_id,
report_path=report_path, update=update)
L... | [
"Add",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/load/report.py#L14-L26 | [
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"c... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_peddy_ped | Parse a peddy.ped file
Args:
lines(iterable(str))
Returns:
peddy_ped(list(dict)) | scout/parse/peddy.py | def parse_peddy_ped(lines):
"""Parse a peddy.ped file
Args:
lines(iterable(str))
Returns:
peddy_ped(list(dict))
"""
peddy_ped = []
header = []
for i,line in enumerate(lines):
line = line.rstrip()
if i == 0:
# Header line
heade... | def parse_peddy_ped(lines):
"""Parse a peddy.ped file
Args:
lines(iterable(str))
Returns:
peddy_ped(list(dict))
"""
peddy_ped = []
header = []
for i,line in enumerate(lines):
line = line.rstrip()
if i == 0:
# Header line
heade... | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_peddy_ped_check | Parse a .ped_check.csv file
Args:
lines(iterable(str))
Returns:
ped_check(list(dict)) | scout/parse/peddy.py | def parse_peddy_ped_check(lines):
"""Parse a .ped_check.csv file
Args:
lines(iterable(str))
Returns:
ped_check(list(dict))
"""
ped_check = []
header = []
for i,line in enumerate(lines):
line = line.rstrip()
if i == 0:
# Header line
... | def parse_peddy_ped_check(lines):
"""Parse a .ped_check.csv file
Args:
lines(iterable(str))
Returns:
ped_check(list(dict))
"""
ped_check = []
header = []
for i,line in enumerate(lines):
line = line.rstrip()
if i == 0:
# Header line
... | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_peddy_sex_check | Parse a .ped_check.csv file
Args:
lines(iterable(str))
Returns:
sex_check(list(dict)) | scout/parse/peddy.py | def parse_peddy_sex_check(lines):
"""Parse a .ped_check.csv file
Args:
lines(iterable(str))
Returns:
sex_check(list(dict))
"""
sex_check = []
header = []
for i,line in enumerate(lines):
line = line.rstrip()
if i == 0:
# Header line
... | def parse_peddy_sex_check(lines):
"""Parse a .ped_check.csv file
Args:
lines(iterable(str))
Returns:
sex_check(list(dict))
"""
sex_check = []
header = []
for i,line in enumerate(lines):
line = line.rstrip()
if i == 0:
# Header line
... | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | hpo_terms | Retrieves a list of HPO terms from scout database
Args:
store (obj): an adapter to the scout database
query (str): the term to search in the database
limit (str): the number of desired results
Returns:
hpo_phenotypes (dict): the complete list of HPO objects stored in scout | scout/server/blueprints/phenotypes/controllers.py | def hpo_terms(store, query = None, limit = None):
"""Retrieves a list of HPO terms from scout database
Args:
store (obj): an adapter to the scout database
query (str): the term to search in the database
limit (str): the number of desired results
Returns:
hpo_phenotypes (dic... | def hpo_terms(store, query = None, limit = None):
"""Retrieves a list of HPO terms from scout database
Args:
store (obj): an adapter to the scout database
query (str): the term to search in the database
limit (str): the number of desired results
Returns:
hpo_phenotypes (dic... | [
"Retrieves",
"a",
"list",
"of",
"HPO",
"terms",
"from",
"scout",
"database"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/phenotypes/controllers.py#L3-L20 | [
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test | whitelist | Show all objects in the whitelist collection | scout/commands/view/whitelist.py | def whitelist(context):
"""Show all objects in the whitelist collection"""
LOG.info("Running scout view users")
adapter = context.obj['adapter']
## TODO add a User interface to the adapter
for whitelist_obj in adapter.whitelist_collection.find():
click.echo(whitelist_obj['_id']) | def whitelist(context):
"""Show all objects in the whitelist collection"""
LOG.info("Running scout view users")
adapter = context.obj['adapter']
## TODO add a User interface to the adapter
for whitelist_obj in adapter.whitelist_collection.find():
click.echo(whitelist_obj['_id']) | [
"Show",
"all",
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"in",
"the",
"whitelist",
"collection"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/view/whitelist.py#L9-L16 | [
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test | build_phenotype | Build a small phenotype object
Build a dictionary with phenotype_id and description
Args:
phenotype_id (str): The phenotype id
adapter (scout.adapter.MongoAdapter)
Returns:
phenotype_obj (dict):
dict(
phenotype_id = str,
feature = str, # descri... | scout/build/case.py | def build_phenotype(phenotype_id, adapter):
"""Build a small phenotype object
Build a dictionary with phenotype_id and description
Args:
phenotype_id (str): The phenotype id
adapter (scout.adapter.MongoAdapter)
Returns:
phenotype_obj (dict):
dict(
phen... | def build_phenotype(phenotype_id, adapter):
"""Build a small phenotype object
Build a dictionary with phenotype_id and description
Args:
phenotype_id (str): The phenotype id
adapter (scout.adapter.MongoAdapter)
Returns:
phenotype_obj (dict):
dict(
phen... | [
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"phenotype",
"object"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/build/case.py#L11-L33 | [
"def",
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"phenotype_obj",
"[",
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"]",
"=",
"phenotyp... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | build_case | Build a case object that is to be inserted to the database
Args:
case_data (dict): A dictionary with the relevant case information
adapter (scout.adapter.MongoAdapter)
Returns:
case_obj (dict): A case object
dict(
case_id = str, # required=True, unique
display_name... | scout/build/case.py | def build_case(case_data, adapter):
"""Build a case object that is to be inserted to the database
Args:
case_data (dict): A dictionary with the relevant case information
adapter (scout.adapter.MongoAdapter)
Returns:
case_obj (dict): A case object
dict(
case_id = str, #... | def build_case(case_data, adapter):
"""Build a case object that is to be inserted to the database
Args:
case_data (dict): A dictionary with the relevant case information
adapter (scout.adapter.MongoAdapter)
Returns:
case_obj (dict): A case object
dict(
case_id = str, #... | [
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"be",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/build/case.py#L35-L239 | [
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"[",
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"]... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | gene | Parse information about a gene. | scout/server/blueprints/genes/controllers.py | def gene(store, hgnc_id):
"""Parse information about a gene."""
res = {'builds': {'37': None, '38': None}, 'symbol': None, 'description': None, 'ensembl_id': None, 'record': None}
for build in res['builds']:
record = store.hgnc_gene(hgnc_id, build=build)
if record:
record['posi... | def gene(store, hgnc_id):
"""Parse information about a gene."""
res = {'builds': {'37': None, '38': None}, 'symbol': None, 'description': None, 'ensembl_id': None, 'record': None}
for build in res['builds']:
record = store.hgnc_gene(hgnc_id, build=build)
if record:
record['posi... | [
"Parse",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/genes/controllers.py#L6-L44 | [
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","... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | genes_to_json | Fetch matching genes and convert to JSON. | scout/server/blueprints/genes/controllers.py | def genes_to_json(store, query):
"""Fetch matching genes and convert to JSON."""
gene_query = store.hgnc_genes(query, search=True)
json_terms = [{'name': "{} | {} ({})".format(gene['hgnc_id'], gene['hgnc_symbol'],
', '.join(gene['aliases'])),
... | def genes_to_json(store, query):
"""Fetch matching genes and convert to JSON."""
gene_query = store.hgnc_genes(query, search=True)
json_terms = [{'name': "{} | {} ({})".format(gene['hgnc_id'], gene['hgnc_symbol'],
', '.join(gene['aliases'])),
... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/genes/controllers.py#L48-L54 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | index | Display the Scout dashboard. | scout/server/blueprints/dashboard/views.py | def index():
"""Display the Scout dashboard."""
accessible_institutes = current_user.institutes
if not 'admin' in current_user.roles:
accessible_institutes = current_user.institutes
if not accessible_institutes:
flash('Not allowed to see information - please visit the dashboard l... | def index():
"""Display the Scout dashboard."""
accessible_institutes = current_user.institutes
if not 'admin' in current_user.roles:
accessible_institutes = current_user.institutes
if not accessible_institutes:
flash('Not allowed to see information - please visit the dashboard l... | [
"Display",
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"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/dashboard/views.py#L18-L70 | [
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".",
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"if",
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"accessible_institutes",
... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | weekday | Simple tag - returns the weekday of the given (year, month, day) or of given (weekday_number).
Usage (in template):
{% weekday 2014 3 3 %}
Result: Mon
Return abbreviation by default. To return full name: pass full=True
{% weekday 2014 3 3 full=True %}
Result: Monday
When only number ... | happenings/templatetags/weekday.py | def weekday(year_or_num, month=None, day=None, full=False):
"""Simple tag - returns the weekday of the given (year, month, day) or of given (weekday_number).
Usage (in template):
{% weekday 2014 3 3 %}
Result: Mon
Return abbreviation by default. To return full name: pass full=True
{% weekda... | def weekday(year_or_num, month=None, day=None, full=False):
"""Simple tag - returns the weekday of the given (year, month, day) or of given (weekday_number).
Usage (in template):
{% weekday 2014 3 3 %}
Result: Mon
Return abbreviation by default. To return full name: pass full=True
{% weekda... | [
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"given",
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] | wreckage/django-happenings | python | https://github.com/wreckage/django-happenings/blob/7bca5576efa6cd4c4e87356bf9e5b8cd538ae91d/happenings/templatetags/weekday.py#L12-L48 | [
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... | 7bca5576efa6cd4c4e87356bf9e5b8cd538ae91d |
test | get_request | Return a requests response from url
Args:
url(str)
Returns:
decoded_data(str): Decoded response | scout/utils/requests.py | def get_request(url):
"""Return a requests response from url
Args:
url(str)
Returns:
decoded_data(str): Decoded response
"""
try:
LOG.info("Requesting %s", url)
response = urllib.request.urlopen(url)
if url.endswith('.gz'):
LOG.info("Deco... | def get_request(url):
"""Return a requests response from url
Args:
url(str)
Returns:
decoded_data(str): Decoded response
"""
try:
LOG.info("Requesting %s", url)
response = urllib.request.urlopen(url)
if url.endswith('.gz'):
LOG.info("Deco... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/utils/requests.py#L15-L43 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | fetch_resource | Fetch a resource and return the resulting lines in a list
Send file_name to get more clean log messages
Args:
url(str)
Returns:
lines(list(str)) | scout/utils/requests.py | def fetch_resource(url):
"""Fetch a resource and return the resulting lines in a list
Send file_name to get more clean log messages
Args:
url(str)
Returns:
lines(list(str))
"""
try:
data = get_request(url)
lines = data.split('\n')
except Exception as... | def fetch_resource(url):
"""Fetch a resource and return the resulting lines in a list
Send file_name to get more clean log messages
Args:
url(str)
Returns:
lines(list(str))
"""
try:
data = get_request(url)
lines = data.split('\n')
except Exception as... | [
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"raise",
"err",
"return",
"lines"
] | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | fetch_mim_files | Fetch the necessary mim files using a api key
Args:
api_key(str): A api key necessary to fetch mim data
Returns:
mim_files(dict): A dictionary with the neccesary files | scout/utils/requests.py | def fetch_mim_files(api_key, mim2genes=False, mimtitles=False, morbidmap=False, genemap2=False):
"""Fetch the necessary mim files using a api key
Args:
api_key(str): A api key necessary to fetch mim data
Returns:
mim_files(dict): A dictionary with the neccesary files
"""
L... | def fetch_mim_files(api_key, mim2genes=False, mimtitles=False, morbidmap=False, genemap2=False):
"""Fetch the necessary mim files using a api key
Args:
api_key(str): A api key necessary to fetch mim data
Returns:
mim_files(dict): A dictionary with the neccesary files
"""
L... | [
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... | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/utils/requests.py#L64-L96 | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | fetch_ensembl_genes | Fetch the ensembl genes
Args:
build(str): ['37', '38'] | scout/utils/requests.py | def fetch_ensembl_genes(build='37'):
"""Fetch the ensembl genes
Args:
build(str): ['37', '38']
"""
if build == '37':
url = 'http://grch37.ensembl.org'
else:
url = 'http://www.ensembl.org'
LOG.info("Fetching ensembl genes from %s", url)
dataset_name = 'hsapie... | def fetch_ensembl_genes(build='37'):
"""Fetch the ensembl genes
Args:
build(str): ['37', '38']
"""
if build == '37':
url = 'http://grch37.ensembl.org'
else:
url = 'http://www.ensembl.org'
LOG.info("Fetching ensembl genes from %s", url)
dataset_name = 'hsapie... | [
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"]"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/utils/requests.py#L144-L179 | [
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",",... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | fetch_ensembl_exons | Fetch the ensembl genes
Args:
build(str): ['37', '38'] | scout/utils/requests.py | def fetch_ensembl_exons(build='37'):
"""Fetch the ensembl genes
Args:
build(str): ['37', '38']
"""
LOG.info("Fetching ensembl exons build %s ...", build)
if build == '37':
url = 'http://grch37.ensembl.org'
else:
url = 'http://www.ensembl.org'
dataset_name = ... | def fetch_ensembl_exons(build='37'):
"""Fetch the ensembl genes
Args:
build(str): ['37', '38']
"""
LOG.info("Fetching ensembl exons build %s ...", build)
if build == '37':
url = 'http://grch37.ensembl.org'
else:
url = 'http://www.ensembl.org'
dataset_name = ... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/utils/requests.py#L225-L265 | [
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"'ht... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | fetch_hgnc | Fetch the hgnc genes file from
ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt
Returns:
hgnc_gene_lines(list(str)) | scout/utils/requests.py | def fetch_hgnc():
"""Fetch the hgnc genes file from
ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt
Returns:
hgnc_gene_lines(list(str))
"""
file_name = "hgnc_complete_set.txt"
url = 'ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/{0}'.format(file_... | def fetch_hgnc():
"""Fetch the hgnc genes file from
ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt
Returns:
hgnc_gene_lines(list(str))
"""
file_name = "hgnc_complete_set.txt"
url = 'ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/{0}'.format(file_... | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | fetch_exac_constraint | Fetch the file with exac constraint scores
Returns:
exac_lines(iterable(str)) | scout/utils/requests.py | def fetch_exac_constraint():
"""Fetch the file with exac constraint scores
Returns:
exac_lines(iterable(str))
"""
file_name = 'fordist_cleaned_exac_r03_march16_z_pli_rec_null_data.txt'
url = ('ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/functional_gene_constraint'
... | def fetch_exac_constraint():
"""Fetch the file with exac constraint scores
Returns:
exac_lines(iterable(str))
"""
file_name = 'fordist_cleaned_exac_r03_march16_z_pli_rec_null_data.txt'
url = ('ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/functional_gene_constraint'
... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/utils/requests.py#L282-L304 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | fetch_hpo_files | Fetch the necessary mim files using a api key
Args:
api_key(str): A api key necessary to fetch mim data
Returns:
mim_files(dict): A dictionary with the neccesary files | scout/utils/requests.py | def fetch_hpo_files(hpogenes=False, hpoterms=False, phenotype_to_terms=False, hpodisease=False):
"""Fetch the necessary mim files using a api key
Args:
api_key(str): A api key necessary to fetch mim data
Returns:
mim_files(dict): A dictionary with the neccesary files
"""
L... | def fetch_hpo_files(hpogenes=False, hpoterms=False, phenotype_to_terms=False, hpodisease=False):
"""Fetch the necessary mim files using a api key
Args:
api_key(str): A api key necessary to fetch mim data
Returns:
mim_files(dict): A dictionary with the neccesary files
"""
L... | [
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"(",
"\"Fetching HPO information from http://compbio.charite.de\"",
")",
... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | transcripts | Show all transcripts in the database | scout/commands/view/transcripts.py | def transcripts(context, build, hgnc_id, json):
"""Show all transcripts in the database"""
LOG.info("Running scout view transcripts")
adapter = context.obj['adapter']
if not json:
click.echo("Chromosome\tstart\tend\ttranscript_id\thgnc_id\trefseq\tis_primary")
for tx_obj in adapter.transcri... | def transcripts(context, build, hgnc_id, json):
"""Show all transcripts in the database"""
LOG.info("Running scout view transcripts")
adapter = context.obj['adapter']
if not json:
click.echo("Chromosome\tstart\tend\ttranscript_id\thgnc_id\trefseq\tis_primary")
for tx_obj in adapter.transcri... | [
"Show",
"all",
"transcripts",
"in",
"the",
"database"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/commands/view/transcripts.py#L13-L32 | [
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"]",
"if",
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"json",
":",
"click",
... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | add_occurrences | Adds an occurrence key to the event object w/ a list of occurrences
and adds a popover (for use with twitter bootstrap).
The occurrence is added so that each event can be aware of what
day(s) it occurs in the month. | happenings/utils/displays.py | def add_occurrences(events, count):
"""
Adds an occurrence key to the event object w/ a list of occurrences
and adds a popover (for use with twitter bootstrap).
The occurrence is added so that each event can be aware of what
day(s) it occurs in the month.
"""
for day in count:
for it... | def add_occurrences(events, count):
"""
Adds an occurrence key to the event object w/ a list of occurrences
and adds a popover (for use with twitter bootstrap).
The occurrence is added so that each event can be aware of what
day(s) it occurs in the month.
"""
for day in count:
for it... | [
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... | wreckage/django-happenings | python | https://github.com/wreckage/django-happenings/blob/7bca5576efa6cd4c4e87356bf9e5b8cd538ae91d/happenings/utils/displays.py#L25-L40 | [
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"==",
"item",
"[",
"1",
"]",
":"... | 7bca5576efa6cd4c4e87356bf9e5b8cd538ae91d |
test | month_display | A function that returns an html calendar for the given
month in the given year, with the number of events for that month
shown on the generated calendar. Start_day is the day the calendar
should start on (default is Monday). | happenings/utils/displays.py | def month_display(year, month, all_month_events,
start_day, net, qs, mini=False, request=None, context=None):
"""
A function that returns an html calendar for the given
month in the given year, with the number of events for that month
shown on the generated calendar. Start_day is the d... | def month_display(year, month, all_month_events,
start_day, net, qs, mini=False, request=None, context=None):
"""
A function that returns an html calendar for the given
month in the given year, with the number of events for that month
shown on the generated calendar. Start_day is the d... | [
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"shown",
"on",
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"generated",
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".",
"Start_day",
"i... | wreckage/django-happenings | python | https://github.com/wreckage/django-happenings/blob/7bca5576efa6cd4c4e87356bf9e5b8cd538ae91d/happenings/utils/displays.py#L43-L83 | [
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"=",
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")",
":",
"# count the number of times events happen on a ... | 7bca5576efa6cd4c4e87356bf9e5b8cd538ae91d |
test | day_display | Returns the events that occur on the given day.
Works by getting all occurrences for the month, then drilling
down to only those occurring on the given day. | happenings/utils/displays.py | def day_display(year, month, all_month_events, day):
"""
Returns the events that occur on the given day.
Works by getting all occurrences for the month, then drilling
down to only those occurring on the given day.
"""
# Get a dict with all of the events for the month
count = CountHandler(yea... | def day_display(year, month, all_month_events, day):
"""
Returns the events that occur on the given day.
Works by getting all occurrences for the month, then drilling
down to only those occurring on the given day.
"""
# Get a dict with all of the events for the month
count = CountHandler(yea... | [
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] | wreckage/django-happenings | python | https://github.com/wreckage/django-happenings/blob/7bca5576efa6cd4c4e87356bf9e5b8cd538ae91d/happenings/utils/displays.py#L86-L100 | [
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... | 7bca5576efa6cd4c4e87356bf9e5b8cd538ae91d |
test | variants | Pre-process list of variants. | scout/server/blueprints/variants/controllers.py | def variants(store, institute_obj, case_obj, variants_query, page=1, per_page=50):
"""Pre-process list of variants."""
variant_count = variants_query.count()
skip_count = per_page * max(page - 1, 0)
more_variants = True if variant_count > (skip_count + per_page) else False
variant_res = variants_que... | def variants(store, institute_obj, case_obj, variants_query, page=1, per_page=50):
"""Pre-process list of variants."""
variant_count = variants_query.count()
skip_count = per_page * max(page - 1, 0)
more_variants = True if variant_count > (skip_count + per_page) else False
variant_res = variants_que... | [
"Pre",
"-",
"process",
"list",
"of",
"variants",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L34-L55 | [
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"*",
... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | sv_variants | Pre-process list of SV variants. | scout/server/blueprints/variants/controllers.py | def sv_variants(store, institute_obj, case_obj, variants_query, page=1, per_page=50):
"""Pre-process list of SV variants."""
skip_count = (per_page * max(page - 1, 0))
more_variants = True if variants_query.count() > (skip_count + per_page) else False
genome_build = case_obj.get('genome_build', '37')
... | def sv_variants(store, institute_obj, case_obj, variants_query, page=1, per_page=50):
"""Pre-process list of SV variants."""
skip_count = (per_page * max(page - 1, 0))
more_variants = True if variants_query.count() > (skip_count + per_page) else False
genome_build = case_obj.get('genome_build', '37')
... | [
"Pre",
"-",
"process",
"list",
"of",
"SV",
"variants",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L57-L70 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | str_variants | Pre-process list of STR variants. | scout/server/blueprints/variants/controllers.py | def str_variants(store, institute_obj, case_obj, variants_query, page=1, per_page=50):
"""Pre-process list of STR variants."""
# Nothing unique to STRs on this level. Inheritance?
return variants(store, institute_obj, case_obj, variants_query, page, per_page) | def str_variants(store, institute_obj, case_obj, variants_query, page=1, per_page=50):
"""Pre-process list of STR variants."""
# Nothing unique to STRs on this level. Inheritance?
return variants(store, institute_obj, case_obj, variants_query, page, per_page) | [
"Pre",
"-",
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"of",
"STR",
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"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L72-L75 | [
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"return",
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"instit... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | str_variant | Pre-process an STR variant entry for detail page.
Adds information to display variant
Args:
store(scout.adapter.MongoAdapter)
institute_id(str)
case_name(str)
variant_id(str)
Returns:
detailed_information(dict): {
'institute': <institute_obj>,
... | scout/server/blueprints/variants/controllers.py | def str_variant(store, institute_id, case_name, variant_id):
"""Pre-process an STR variant entry for detail page.
Adds information to display variant
Args:
store(scout.adapter.MongoAdapter)
institute_id(str)
case_name(str)
variant_id(str)
Returns:
detailed_info... | def str_variant(store, institute_id, case_name, variant_id):
"""Pre-process an STR variant entry for detail page.
Adds information to display variant
Args:
store(scout.adapter.MongoAdapter)
institute_id(str)
case_name(str)
variant_id(str)
Returns:
detailed_info... | [
"Pre",
"-",
"process",
"an",
"STR",
"variant",
"entry",
"for",
"detail",
"page",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L77-L121 | [
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")",
"variant_obj",
"=",
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".",
"va... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | sv_variant | Pre-process an SV variant entry for detail page.
Adds information to display variant
Args:
store(scout.adapter.MongoAdapter)
institute_id(str)
case_name(str)
variant_id(str)
variant_obj(dcit)
add_case(bool): If information about case files should be added
R... | scout/server/blueprints/variants/controllers.py | def sv_variant(store, institute_id, case_name, variant_id=None, variant_obj=None, add_case=True,
get_overlapping=True):
"""Pre-process an SV variant entry for detail page.
Adds information to display variant
Args:
store(scout.adapter.MongoAdapter)
institute_id(str)
c... | def sv_variant(store, institute_id, case_name, variant_id=None, variant_obj=None, add_case=True,
get_overlapping=True):
"""Pre-process an SV variant entry for detail page.
Adds information to display variant
Args:
store(scout.adapter.MongoAdapter)
institute_id(str)
c... | [
"Pre",
"-",
"process",
"an",
"SV",
"variant",
"entry",
"for",
"detail",
"page",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L123-L202 | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_variant | Parse information about variants.
- Adds information about compounds
- Updates the information about compounds if necessary and 'update=True'
Args:
store(scout.adapter.MongoAdapter)
institute_obj(scout.models.Institute)
case_obj(scout.models.Case)
variant_obj(scout.models.V... | scout/server/blueprints/variants/controllers.py | def parse_variant(store, institute_obj, case_obj, variant_obj, update=False, genome_build='37',
get_compounds = True):
"""Parse information about variants.
- Adds information about compounds
- Updates the information about compounds if necessary and 'update=True'
Args:
store(... | def parse_variant(store, institute_obj, case_obj, variant_obj, update=False, genome_build='37',
get_compounds = True):
"""Parse information about variants.
- Adds information about compounds
- Updates the information about compounds if necessary and 'update=True'
Args:
store(... | [
"Parse",
"information",
"about",
"variants",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L205-L277 | [
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"=",
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"compounds",
"=",
"varia... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | variant_export_lines | Get variants info to be exported to file, one list (line) per variant.
Args:
store(scout.adapter.MongoAdapter)
case_obj(scout.models.Case)
variants_query: a list of variant objects, each one is a dictionary
Returns:
export_variants: a list of strings. Ea... | scout/server/blueprints/variants/controllers.py | def variant_export_lines(store, case_obj, variants_query):
"""Get variants info to be exported to file, one list (line) per variant.
Args:
store(scout.adapter.MongoAdapter)
case_obj(scout.models.Case)
variants_query: a list of variant objects, each one is a dictionary
... | def variant_export_lines(store, case_obj, variants_query):
"""Get variants info to be exported to file, one list (line) per variant.
Args:
store(scout.adapter.MongoAdapter)
case_obj(scout.models.Case)
variants_query: a list of variant objects, each one is a dictionary
... | [
"Get",
"variants",
"info",
"to",
"be",
"exported",
"to",
"file",
"one",
"list",
"(",
"line",
")",
"per",
"variant",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L280-L349 | [
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"]",
... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | variants_export_header | Returns a header for the CSV file with the filtered variants to be exported.
Args:
case_obj(scout.models.Case)
Returns:
header: includes the fields defined in scout.constants.variants_export EXPORT_HEADER
+ AD_reference, AD_alternate, GT_quality for each sam... | scout/server/blueprints/variants/controllers.py | def variants_export_header(case_obj):
"""Returns a header for the CSV file with the filtered variants to be exported.
Args:
case_obj(scout.models.Case)
Returns:
header: includes the fields defined in scout.constants.variants_export EXPORT_HEADER
+ AD_ref... | def variants_export_header(case_obj):
"""Returns a header for the CSV file with the filtered variants to be exported.
Args:
case_obj(scout.models.Case)
Returns:
header: includes the fields defined in scout.constants.variants_export EXPORT_HEADER
+ AD_ref... | [
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"CSV",
"file",
"with",
"the",
"filtered",
"variants",
"to",
"be",
"exported",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L352-L370 | [
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"display_name",
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | get_variant_info | Get variant information | scout/server/blueprints/variants/controllers.py | def get_variant_info(genes):
"""Get variant information"""
data = {'canonical_transcripts': []}
for gene_obj in genes:
if not gene_obj.get('canonical_transcripts'):
tx = gene_obj['transcripts'][0]
tx_id = tx['transcript_id']
exon = tx.get('exon', '-')
... | def get_variant_info(genes):
"""Get variant information"""
data = {'canonical_transcripts': []}
for gene_obj in genes:
if not gene_obj.get('canonical_transcripts'):
tx = gene_obj['transcripts'][0]
tx_id = tx['transcript_id']
exon = tx.get('exon', '-')
... | [
"Get",
"variant",
"information"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L373-L397 | [
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"gene_obj",... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | get_predictions | Get sift predictions from genes. | scout/server/blueprints/variants/controllers.py | def get_predictions(genes):
"""Get sift predictions from genes."""
data = {
'sift_predictions': [],
'polyphen_predictions': [],
'region_annotations': [],
'functional_annotations': []
}
for gene_obj in genes:
for pred_key in data:
gene_key = pred_key[:-... | def get_predictions(genes):
"""Get sift predictions from genes."""
data = {
'sift_predictions': [],
'polyphen_predictions': [],
'region_annotations': [],
'functional_annotations': []
}
for gene_obj in genes:
for pred_key in data:
gene_key = pred_key[:-... | [
"Get",
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"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L400-L418 | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | variant_case | Pre-process case for the variant view.
Adds information about files from case obj to variant
Args:
store(scout.adapter.MongoAdapter)
case_obj(scout.models.Case)
variant_obj(scout.models.Variant) | scout/server/blueprints/variants/controllers.py | def variant_case(store, case_obj, variant_obj):
"""Pre-process case for the variant view.
Adds information about files from case obj to variant
Args:
store(scout.adapter.MongoAdapter)
case_obj(scout.models.Case)
variant_obj(scout.models.Variant)
"""
case_obj['bam_files'] = ... | def variant_case(store, case_obj, variant_obj):
"""Pre-process case for the variant view.
Adds information about files from case obj to variant
Args:
store(scout.adapter.MongoAdapter)
case_obj(scout.models.Case)
variant_obj(scout.models.Variant)
"""
case_obj['bam_files'] = ... | [
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"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L421-L467 | [
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test | find_bai_file | Find out BAI file by extension given the BAM file. | scout/server/blueprints/variants/controllers.py | def find_bai_file(bam_file):
"""Find out BAI file by extension given the BAM file."""
bai_file = bam_file.replace('.bam', '.bai')
if not os.path.exists(bai_file):
# try the other convention
bai_file = "{}.bai".format(bam_file)
return bai_file | def find_bai_file(bam_file):
"""Find out BAI file by extension given the BAM file."""
bai_file = bam_file.replace('.bam', '.bai')
if not os.path.exists(bai_file):
# try the other convention
bai_file = "{}.bai".format(bam_file)
return bai_file | [
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"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L470-L476 | [
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test | variant | Pre-process a single variant for the detailed variant view.
Adds information from case and institute that is not present on the variant
object
Args:
store(scout.adapter.MongoAdapter)
institute_obj(scout.models.Institute)
case_obj(scout.models.Case)
variant_id(str)
v... | scout/server/blueprints/variants/controllers.py | def variant(store, institute_obj, case_obj, variant_id=None, variant_obj=None, add_case=True,
add_other=True, get_overlapping=True):
"""Pre-process a single variant for the detailed variant view.
Adds information from case and institute that is not present on the variant
object
Args:
... | def variant(store, institute_obj, case_obj, variant_id=None, variant_obj=None, add_case=True,
add_other=True, get_overlapping=True):
"""Pre-process a single variant for the detailed variant view.
Adds information from case and institute that is not present on the variant
object
Args:
... | [
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"-",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L479-L629 | [
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test | observations | Query observations for a variant. | scout/server/blueprints/variants/controllers.py | def observations(store, loqusdb, case_obj, variant_obj):
"""Query observations for a variant."""
composite_id = ("{this[chromosome]}_{this[position]}_{this[reference]}_"
"{this[alternative]}".format(this=variant_obj))
obs_data = loqusdb.get_variant({'_id': composite_id}) or {}
obs_da... | def observations(store, loqusdb, case_obj, variant_obj):
"""Query observations for a variant."""
composite_id = ("{this[chromosome]}_{this[position]}_{this[reference]}_"
"{this[alternative]}".format(this=variant_obj))
obs_data = loqusdb.get_variant({'_id': composite_id}) or {}
obs_da... | [
"Query",
"observations",
"for",
"a",
"variant",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L631-L646 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | parse_gene | Parse variant genes. | scout/server/blueprints/variants/controllers.py | def parse_gene(gene_obj, build=None):
"""Parse variant genes."""
build = build or 37
if gene_obj.get('common'):
add_gene_links(gene_obj, build)
refseq_transcripts = []
for tx_obj in gene_obj['transcripts']:
parse_transcript(gene_obj, tx_obj, build)
# select ... | def parse_gene(gene_obj, build=None):
"""Parse variant genes."""
build = build or 37
if gene_obj.get('common'):
add_gene_links(gene_obj, build)
refseq_transcripts = []
for tx_obj in gene_obj['transcripts']:
parse_transcript(gene_obj, tx_obj, build)
# select ... | [
"Parse",
"variant",
"genes",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L649-L665 | [
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test | parse_transcript | Parse variant gene transcript (VEP). | scout/server/blueprints/variants/controllers.py | def parse_transcript(gene_obj, tx_obj, build=None):
"""Parse variant gene transcript (VEP)."""
build = build or 37
add_tx_links(tx_obj, build)
if tx_obj.get('refseq_id'):
gene_name = (gene_obj['common']['hgnc_symbol'] if gene_obj['common'] else
gene_obj['hgnc_id'])
... | def parse_transcript(gene_obj, tx_obj, build=None):
"""Parse variant gene transcript (VEP)."""
build = build or 37
add_tx_links(tx_obj, build)
if tx_obj.get('refseq_id'):
gene_name = (gene_obj['common']['hgnc_symbol'] if gene_obj['common'] else
gene_obj['hgnc_id'])
... | [
"Parse",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L667-L675 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | transcript_str | Generate amino acid change as a string. | scout/server/blueprints/variants/controllers.py | def transcript_str(transcript_obj, gene_name=None):
"""Generate amino acid change as a string."""
if transcript_obj.get('exon'):
gene_part, part_count_raw = 'exon', transcript_obj['exon']
elif transcript_obj.get('intron'):
gene_part, part_count_raw = 'intron', transcript_obj['intron']
el... | def transcript_str(transcript_obj, gene_name=None):
"""Generate amino acid change as a string."""
if transcript_obj.get('exon'):
gene_part, part_count_raw = 'exon', transcript_obj['exon']
elif transcript_obj.get('intron'):
gene_part, part_count_raw = 'intron', transcript_obj['intron']
el... | [
"Generate",
"amino",
"acid",
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"as",
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"string",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L677-L697 | [
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test | end_position | Calculate end position for a variant. | scout/server/blueprints/variants/controllers.py | def end_position(variant_obj):
"""Calculate end position for a variant."""
alt_bases = len(variant_obj['alternative'])
num_bases = max(len(variant_obj['reference']), alt_bases)
return variant_obj['position'] + (num_bases - 1) | def end_position(variant_obj):
"""Calculate end position for a variant."""
alt_bases = len(variant_obj['alternative'])
num_bases = max(len(variant_obj['reference']), alt_bases)
return variant_obj['position'] + (num_bases - 1) | [
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"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L700-L704 | [
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test | frequency | Returns a judgement on the overall frequency of the variant.
Combines multiple metrics into a single call. | scout/server/blueprints/variants/controllers.py | def frequency(variant_obj):
"""Returns a judgement on the overall frequency of the variant.
Combines multiple metrics into a single call.
"""
most_common_frequency = max(variant_obj.get('thousand_genomes_frequency') or 0,
variant_obj.get('exac_frequency') or 0)
if mo... | def frequency(variant_obj):
"""Returns a judgement on the overall frequency of the variant.
Combines multiple metrics into a single call.
"""
most_common_frequency = max(variant_obj.get('thousand_genomes_frequency') or 0,
variant_obj.get('exac_frequency') or 0)
if mo... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L707-L719 | [
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test | clinsig_human | Convert to human readable version of CLINSIG evaluation. | scout/server/blueprints/variants/controllers.py | def clinsig_human(variant_obj):
"""Convert to human readable version of CLINSIG evaluation."""
for clinsig_obj in variant_obj['clnsig']:
# The clinsig objects allways have a accession
if isinstance(clinsig_obj['accession'], int):
# New version
link = "https://www.ncbi.nlm... | def clinsig_human(variant_obj):
"""Convert to human readable version of CLINSIG evaluation."""
for clinsig_obj in variant_obj['clnsig']:
# The clinsig objects allways have a accession
if isinstance(clinsig_obj['accession'], int):
# New version
link = "https://www.ncbi.nlm... | [
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"CLINSIG",
"evaluation",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L722-L746 | [
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test | thousandg_link | Compose link to 1000G page for detailed information. | scout/server/blueprints/variants/controllers.py | def thousandg_link(variant_obj, build=None):
"""Compose link to 1000G page for detailed information."""
dbsnp_id = variant_obj.get('dbsnp_id')
build = build or 37
if not dbsnp_id:
return None
if build == 37:
url_template = ("http://grch37.ensembl.org/Homo_sapiens/Variation/Explore"... | def thousandg_link(variant_obj, build=None):
"""Compose link to 1000G page for detailed information."""
dbsnp_id = variant_obj.get('dbsnp_id')
build = build or 37
if not dbsnp_id:
return None
if build == 37:
url_template = ("http://grch37.ensembl.org/Homo_sapiens/Variation/Explore"... | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | cosmic_link | Compose link to COSMIC Database.
Args:
variant_obj(scout.models.Variant)
Returns:
url_template(str): Link to COSMIIC database if cosmic id is present | scout/server/blueprints/variants/controllers.py | def cosmic_link(variant_obj):
"""Compose link to COSMIC Database.
Args:
variant_obj(scout.models.Variant)
Returns:
url_template(str): Link to COSMIIC database if cosmic id is present
"""
cosmic_ids = variant_obj.get('cosmic_ids')
if not cosmic_ids:
return None
els... | def cosmic_link(variant_obj):
"""Compose link to COSMIC Database.
Args:
variant_obj(scout.models.Variant)
Returns:
url_template(str): Link to COSMIIC database if cosmic id is present
"""
cosmic_ids = variant_obj.get('cosmic_ids')
if not cosmic_ids:
return None
els... | [
"Compose",
"link",
"to",
"COSMIC",
"Database",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L788-L807 | [
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test | beacon_link | Compose link to Beacon Network. | scout/server/blueprints/variants/controllers.py | def beacon_link(variant_obj, build=None):
"""Compose link to Beacon Network."""
build = build or 37
url_template = ("https://beacon-network.org/#/search?pos={this[position]}&"
"chrom={this[chromosome]}&allele={this[alternative]}&"
"ref={this[reference]}&rs=GRCh37")
... | def beacon_link(variant_obj, build=None):
"""Compose link to Beacon Network."""
build = build or 37
url_template = ("https://beacon-network.org/#/search?pos={this[position]}&"
"chrom={this[chromosome]}&allele={this[alternative]}&"
"ref={this[reference]}&rs=GRCh37")
... | [
"Compose",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L809-L821 | [
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test | ucsc_link | Compose link to UCSC. | scout/server/blueprints/variants/controllers.py | def ucsc_link(variant_obj, build=None):
"""Compose link to UCSC."""
build = build or 37
url_template = ("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&"
"position=chr{this[chromosome]}:{this[position]}"
"-{this[position]}&dgv=pack&knownGene=pack&omimGene=pac... | def ucsc_link(variant_obj, build=None):
"""Compose link to UCSC."""
build = build or 37
url_template = ("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&"
"position=chr{this[chromosome]}:{this[position]}"
"-{this[position]}&dgv=pack&knownGene=pack&omimGene=pac... | [
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"\"-{this[position]}&dgv=pa... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | spidex_human | Translate SPIDEX annotation to human readable string. | scout/server/blueprints/variants/controllers.py | def spidex_human(variant_obj):
"""Translate SPIDEX annotation to human readable string."""
if variant_obj.get('spidex') is None:
return 'not_reported'
elif abs(variant_obj['spidex']) < SPIDEX_HUMAN['low']['pos'][1]:
return 'low'
elif abs(variant_obj['spidex']) < SPIDEX_HUMAN['medium']['p... | def spidex_human(variant_obj):
"""Translate SPIDEX annotation to human readable string."""
if variant_obj.get('spidex') is None:
return 'not_reported'
elif abs(variant_obj['spidex']) < SPIDEX_HUMAN['low']['pos'][1]:
return 'low'
elif abs(variant_obj['spidex']) < SPIDEX_HUMAN['medium']['p... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L844-L853 | [
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"]",... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | expected_inheritance | Gather information from common gene information. | scout/server/blueprints/variants/controllers.py | def expected_inheritance(variant_obj):
"""Gather information from common gene information."""
manual_models = set()
for gene in variant_obj.get('genes', []):
manual_models.update(gene.get('manual_inheritance', []))
return list(manual_models) | def expected_inheritance(variant_obj):
"""Gather information from common gene information."""
manual_models = set()
for gene in variant_obj.get('genes', []):
manual_models.update(gene.get('manual_inheritance', []))
return list(manual_models) | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L856-L861 | [
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | callers | Return info about callers. | scout/server/blueprints/variants/controllers.py | def callers(variant_obj, category='snv'):
"""Return info about callers."""
calls = set()
for caller in CALLERS[category]:
if variant_obj.get(caller['id']):
calls.add((caller['name'], variant_obj[caller['id']]))
return list(calls) | def callers(variant_obj, category='snv'):
"""Return info about callers."""
calls = set()
for caller in CALLERS[category]:
if variant_obj.get(caller['id']):
calls.add((caller['name'], variant_obj[caller['id']]))
return list(calls) | [
"Return",
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"... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | variant_verification | Sand a verification email and register the verification in the database
Args:
store(scout.adapter.MongoAdapter)
mail(scout.server.extensions.mail): an instance of flask_mail.Mail
institute_obj(dict): an institute object
case_obj(dict): a case object
u... | scout/server/blueprints/variants/controllers.py | def variant_verification(store, mail, institute_obj, case_obj, user_obj, variant_obj, sender, variant_url, order, comment, url_builder=url_for):
"""Sand a verification email and register the verification in the database
Args:
store(scout.adapter.MongoAdapter)
mail(scout.server.exten... | def variant_verification(store, mail, institute_obj, case_obj, user_obj, variant_obj, sender, variant_url, order, comment, url_builder=url_for):
"""Sand a verification email and register the verification in the database
Args:
store(scout.adapter.MongoAdapter)
mail(scout.server.exten... | [
"Sand",
"a",
"verification",
"email",
"and",
"register",
"the",
"verification",
"in",
"the",
"database"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L874-L997 | [
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"=",
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | verification_email_body | Builds the html code for the variant verification emails (order verification and cancel verification)
Args:
case_name(str): case display name
url(str): the complete url to the variant, accessible when clicking on the email link
display_name(str): a display name for the varia... | scout/server/blueprints/variants/controllers.py | def verification_email_body(case_name, url, display_name, category, subcategory, breakpoint_1, breakpoint_2, hgnc_symbol, panels, gtcalls, tx_changes, name, comment):
"""
Builds the html code for the variant verification emails (order verification and cancel verification)
Args:
case_nam... | def verification_email_body(case_name, url, display_name, category, subcategory, breakpoint_1, breakpoint_2, hgnc_symbol, panels, gtcalls, tx_changes, name, comment):
"""
Builds the html code for the variant verification emails (order verification and cancel verification)
Args:
case_nam... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L1000-L1055 | [
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"comment",... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | cancer_variants | Fetch data related to cancer variants for a case. | scout/server/blueprints/variants/controllers.py | def cancer_variants(store, request_args, institute_id, case_name):
"""Fetch data related to cancer variants for a case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
form = CancerFiltersForm(request_args)
variants_query = store.variants(case_obj['_id'], category='cancer... | def cancer_variants(store, request_args, institute_id, case_name):
"""Fetch data related to cancer variants for a case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
form = CancerFiltersForm(request_args)
variants_query = store.variants(case_obj['_id'], category='cancer... | [
"Fetch",
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"to",
"cancer",
"variants",
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"a",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L1058-L1071 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | clinvar_export | Gather the required data for creating the clinvar submission form
Args:
store(scout.adapter.MongoAdapter)
institute_id(str): Institute ID
case_name(str): case ID
variant_id(str): variant._id
Returns:
a dictionary with all the required data (c... | scout/server/blueprints/variants/controllers.py | def clinvar_export(store, institute_id, case_name, variant_id):
"""Gather the required data for creating the clinvar submission form
Args:
store(scout.adapter.MongoAdapter)
institute_id(str): Institute ID
case_name(str): case ID
variant_id(str): variant._id
... | def clinvar_export(store, institute_id, case_name, variant_id):
"""Gather the required data for creating the clinvar submission form
Args:
store(scout.adapter.MongoAdapter)
institute_id(str): Institute ID
case_name(str): case ID
variant_id(str): variant._id
... | [
"Gather",
"the",
"required",
"data",
"for",
"creating",
"the",
"clinvar",
"submission",
"form"
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L1073-L1097 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | get_clinvar_submission | Collects all variants from the clinvar submission collection with a specific submission_id
Args:
store(scout.adapter.MongoAdapter)
institute_id(str): Institute ID
case_name(str): case ID
variant_id(str): variant._id
submission_id(str): clinvar submiss... | scout/server/blueprints/variants/controllers.py | def get_clinvar_submission(store, institute_id, case_name, variant_id, submission_id):
"""Collects all variants from the clinvar submission collection with a specific submission_id
Args:
store(scout.adapter.MongoAdapter)
institute_id(str): Institute ID
case_name(str): ca... | def get_clinvar_submission(store, institute_id, case_name, variant_id, submission_id):
"""Collects all variants from the clinvar submission collection with a specific submission_id
Args:
store(scout.adapter.MongoAdapter)
institute_id(str): Institute ID
case_name(str): ca... | [
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"submission",
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L1099-L1125 | [
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test | variant_acmg | Collect data relevant for rendering ACMG classification form. | scout/server/blueprints/variants/controllers.py | def variant_acmg(store, institute_id, case_name, variant_id):
"""Collect data relevant for rendering ACMG classification form."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
return dict(institute=institute_obj, case=case_obj, varia... | def variant_acmg(store, institute_id, case_name, variant_id):
"""Collect data relevant for rendering ACMG classification form."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
return dict(institute=institute_obj, case=case_obj, varia... | [
"Collect",
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"rendering",
"ACMG",
"classification",
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"v... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | variant_acmg_post | Calculate an ACMG classification based on a list of criteria. | scout/server/blueprints/variants/controllers.py | def variant_acmg_post(store, institute_id, case_name, variant_id, user_email, criteria):
"""Calculate an ACMG classification based on a list of criteria."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(user_ema... | def variant_acmg_post(store, institute_id, case_name, variant_id, user_email, criteria):
"""Calculate an ACMG classification based on a list of criteria."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(user_ema... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L1136-L1151 | [
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")... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | evaluation | Fetch and fill-in evaluation object. | scout/server/blueprints/variants/controllers.py | def evaluation(store, evaluation_obj):
"""Fetch and fill-in evaluation object."""
evaluation_obj['institute'] = store.institute(evaluation_obj['institute_id'])
evaluation_obj['case'] = store.case(evaluation_obj['case_id'])
evaluation_obj['variant'] = store.variant(evaluation_obj['variant_specific'])
... | def evaluation(store, evaluation_obj):
"""Fetch and fill-in evaluation object."""
evaluation_obj['institute'] = store.institute(evaluation_obj['institute_id'])
evaluation_obj['case'] = store.case(evaluation_obj['case_id'])
evaluation_obj['variant'] = store.variant(evaluation_obj['variant_specific'])
... | [
"Fetch",
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"object",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L1154-L1162 | [
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"c... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | upload_panel | Parse out HGNC symbols from a stream. | scout/server/blueprints/variants/controllers.py | def upload_panel(store, institute_id, case_name, stream):
"""Parse out HGNC symbols from a stream."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
raw_symbols = [line.strip().split('\t')[0] for line in stream if
line and not line.startswith('#')]
# chec... | def upload_panel(store, institute_id, case_name, stream):
"""Parse out HGNC symbols from a stream."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
raw_symbols = [line.strip().split('\t')[0] for line in stream if
line and not line.startswith('#')]
# chec... | [
"Parse",
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"a",
"stream",
"."
] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L1165-L1177 | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | verified_excel_file | Collect all verified variants in a list on institutes and save them to file
Args:
store(adapter.MongoAdapter)
institute_list(list): a list of institute ids
temp_excel_dir(os.Path): folder where the temp excel files are written to
Returns:
written_files(int): the number of files... | scout/server/blueprints/variants/controllers.py | def verified_excel_file(store, institute_list, temp_excel_dir):
"""Collect all verified variants in a list on institutes and save them to file
Args:
store(adapter.MongoAdapter)
institute_list(list): a list of institute ids
temp_excel_dir(os.Path): folder where the temp excel files are w... | def verified_excel_file(store, institute_list, temp_excel_dir):
"""Collect all verified variants in a list on institutes and save them to file
Args:
store(adapter.MongoAdapter)
institute_list(list): a list of institute ids
temp_excel_dir(os.Path): folder where the temp excel files are w... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/server/blueprints/variants/controllers.py#L1180-L1226 | [
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"'%Y-%m-%d'... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | build_hpo_term | Build a hpo_term object
Check that the information is correct and add the correct hgnc ids to the
array of genes.
Args:
hpo_info(dict)
Returns:
hpo_obj(scout.models.HpoTerm): A dictionary with hpo information | scout/build/hpo.py | def build_hpo_term(hpo_info):
"""Build a hpo_term object
Check that the information is correct and add the correct hgnc ids to the
array of genes.
Args:
hpo_info(dict)
Returns:
hpo_obj(scout.models.HpoTerm): A dictionary with hpo information
... | def build_hpo_term(hpo_info):
"""Build a hpo_term object
Check that the information is correct and add the correct hgnc ids to the
array of genes.
Args:
hpo_info(dict)
Returns:
hpo_obj(scout.models.HpoTerm): A dictionary with hpo information
... | [
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... | 90a551e2e1653a319e654c2405c2866f93d0ebb9 |
test | export_genes | Export all genes from the database | scout/export/gene.py | def export_genes(adapter, build='37'):
"""Export all genes from the database"""
LOG.info("Exporting all genes to .bed format")
for gene_obj in adapter.all_genes(build=build):
yield gene_obj | def export_genes(adapter, build='37'):
"""Export all genes from the database"""
LOG.info("Exporting all genes to .bed format")
for gene_obj in adapter.all_genes(build=build):
yield gene_obj | [
"Export",
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test | parse_clnsig | Get the clnsig information
Args:
acc(str): The clnsig accession number, raw from vcf
sig(str): The clnsig significance score, raw from vcf
revstat(str): The clnsig revstat, raw from vcf
transcripts(iterable(dict))
Returns:
clnsig_accsessions(list): A list with clnsig ac... | scout/parse/variant/clnsig.py | def parse_clnsig(acc, sig, revstat, transcripts):
"""Get the clnsig information
Args:
acc(str): The clnsig accession number, raw from vcf
sig(str): The clnsig significance score, raw from vcf
revstat(str): The clnsig revstat, raw from vcf
transcripts(iterable(dict))
Returns... | def parse_clnsig(acc, sig, revstat, transcripts):
"""Get the clnsig information
Args:
acc(str): The clnsig accession number, raw from vcf
sig(str): The clnsig significance score, raw from vcf
revstat(str): The clnsig revstat, raw from vcf
transcripts(iterable(dict))
Returns... | [
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] | Clinical-Genomics/scout | python | https://github.com/Clinical-Genomics/scout/blob/90a551e2e1653a319e654c2405c2866f93d0ebb9/scout/parse/variant/clnsig.py#L8-L72 | [
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