code string | signature string | docstring string | loss_without_docstring float64 | loss_with_docstring float64 | factor float64 |
|---|---|---|---|---|---|
if out_filename:
params["-out"] = out_filename
#else:
# params["-out"] = get_tmp_filename(WorkingDir)
ih = input_handler or guess_input_handler(seqs, add_seq_names)
muscle_app = Muscle(
params=params,
InputHandler=ih,
Working... | def muscle_seqs(seqs,
add_seq_names=False,
out_filename=None,
input_handler=None,
params={},
WorkingDir=tempfile.gettempdir(),
SuppressStderr=None,
SuppressStdout=None) | Muscle align list of sequences.
seqs: a list of sequences as strings or objects, you must set add_seq_names=True
or sequences in a multiline string, as read() from a fasta file
or sequences in a list of lines, as readlines() from a fasta file
or a fasta seq filename.
== for eg, testcode for guessi... | 3.211449 | 3.391014 | 0.947047 |
num_seqs = len(seqs)
if num_seqs < 2:
raise ValueError, "Muscle requres 2 or more sequences to cluster."
num_chars = sum(map(len, seqs))
if num_chars > max_chars:
params["-maxiters"] = 2
params["-diags1"] = True
params["-sv"] = True
#params["-distance1"] = ... | def cluster_seqs(seqs,
neighbor_join=False,
params={},
add_seq_names=True,
WorkingDir=tempfile.gettempdir(),
SuppressStderr=None,
SuppressStdout=None,
max_chars=1000000,
max_hours=1.0,... | Muscle cluster list of sequences.
seqs: either file name or list of sequence objects or list of strings or
single multiline string containing sequences.
Addl docs coming soon | 4.113131 | 4.089662 | 1.005739 |
params["-maxhours"] = max_hours
if tree_type:
params["-cluster2"] = tree_type
params["-tree2"] = get_tmp_filename(WorkingDir)
params["-out"] = get_tmp_filename(WorkingDir)
muscle_res = muscle_seqs(seqs,
input_handler=input_handler,
params=params,
... | def aln_tree_seqs(seqs,
input_handler=None,
tree_type='neighborjoining',
params={},
add_seq_names=True,
WorkingDir=tempfile.gettempdir(),
SuppressStderr=None,
SuppressStdout=None,
max_... | Muscle align sequences and report tree from iteration2.
Unlike cluster_seqs, returns tree2 which is the tree made during the
second muscle iteration (it should be more accurate that the cluster from
the first iteration which is made fast based on k-mer words)
seqs: either file name or list of sequenc... | 3.099916 | 3.276117 | 0.946216 |
if not params:
params = {}
#create SequenceCollection object from seqs
seq_collection = SequenceCollection(seqs,MolType=moltype)
#Create mapping between abbreviated IDs and full IDs
int_map, int_keys = seq_collection.getIntMap()
#Create SequenceCollection from int_map.
int_map =... | def align_unaligned_seqs(seqs, moltype=DNA, params=None) | Returns an Alignment object from seqs.
seqs: SequenceCollection object, or data that can be used to build one.
moltype: a MolType object. DNA, RNA, or PROTEIN.
params: dict of parameters to pass in to the Muscle app controller.
Result will be an Alignment object. | 4.829744 | 4.716523 | 1.024005 |
aln = align_unaligned_seqs(seqs, moltype=moltype, params=params)
tree = build_tree_from_alignment(aln, moltype, best_tree, params)
return {'Align':aln, 'Tree':tree} | def align_and_build_tree(seqs, moltype, best_tree=False, params=None) | Returns an alignment and a tree from Sequences object seqs.
seqs: a cogent.core.alignment.SequenceCollection object, or data that can
be used to build one.
moltype: cogent.core.moltype.MolType object
best_tree: if True (default:False), uses a slower but more accurate
algorithm to build the tree.
... | 3.264874 | 4.067841 | 0.802606 |
# Create instance of app controller, enable tree, disable alignment
app = Muscle(InputHandler='_input_as_multiline_string', params=params, \
WorkingDir=tempfile.gettempdir())
app.Parameters['-clusteronly'].on()
app.Parameters['-tree1'].on(get_tmp_filename(app.WorkingDir))
ap... | def build_tree_from_alignment(aln, moltype=DNA, best_tree=False, params=None) | Returns a tree from Alignment object aln.
aln: a cogent.core.alignment.Alignment object, or data that can be used
to build one.
moltype: cogent.core.moltype.MolType object
best_tree: unsupported
params: dict of parameters to pass in to the Muscle app controller.
The result will be an cogent... | 7.929642 | 7.37855 | 1.074688 |
if not params:
params = {}
#create SequenceCollection object from seqs
seqs_collection = SequenceCollection(seqs)
#Create mapping between abbreviated IDs and full IDs
seqs_int_map, seqs_int_keys = seqs_collection.getIntMap(prefix='seq_')
#Create SequenceCollection from int_map.
... | def add_seqs_to_alignment(seqs, aln, params=None) | Returns an Alignment object from seqs and existing Alignment.
seqs: a cogent.core.alignment.SequenceCollection object, or data that can
be used to build one.
aln: a cogent.core.alignment.Alignment object, or data that can be used
to build one
params: dict of parameters to pass in to the Muscle ap... | 2.64513 | 2.545307 | 1.039219 |
if not params:
params = {}
#create SequenceCollection object from aln1
aln1_collection = SequenceCollection(aln1)
#Create mapping between abbreviated IDs and full IDs
aln1_int_map, aln1_int_keys = aln1_collection.getIntMap(prefix='aln1_')
#Create SequenceCollection from int_map.
... | def align_two_alignments(aln1, aln2, params=None) | Returns an Alignment object from two existing Alignments.
aln1, aln2: cogent.core.alignment.Alignment objects, or data that can be
used to build them.
params: dict of parameters to pass in to the Muscle app controller. | 2.427089 | 2.357737 | 1.029415 |
if data:
try:
filename1, filename2 = data
except:
raise ValueError, "Expected two filenames"
self.Parameters['-in'].off()
self.Parameters['-in1'].on(filename1)
self.Parameters['-in2'].on(filename2)
retu... | def _input_as_multifile(self, data) | For use with the -profile option
This input handler expects data to be a tuple containing two
filenames. Index 0 will be set to -in1 and index 1 to -in2 | 5.221491 | 4.403486 | 1.185763 |
def get_example():
features = random.sample(string.ascii_letters, NUM_SAMPLES)
num_capitalized = len([ letter for letter in features if letter in string.ascii_uppercase ])
num_lowercase = len([ letter for letter in features if letter in string.ascii_lowercase ])
if num_capitalized > num_lowerc... | Make an example for training and testing. Outputs a tuple
(label, features) where label is +1 if capital letters are the majority,
and -1 otherwise; and features is a list of letters. | null | null | null | |
file_hash = get_cache_buster(redis, path)
return "%s/%s?v=%s" % (oz.settings["static_host"], path, file_hash) | def static_url(redis, path) | Gets the static path for a file | 5.983735 | 6.127131 | 0.976596 |
return escape.to_unicode(redis.hget("cache-buster:{}:v3".format(oz.settings["s3_bucket"]), path)) | def get_cache_buster(redis, path) | Gets the cache buster value for a given file path | 15.628824 | 14.76685 | 1.058372 |
redis.hset("cache-buster:{}:v3".format(oz.settings["s3_bucket"]), path, hash) | def set_cache_buster(redis, path, hash) | Sets the cache buster value for a given file path | 12.336738 | 12.727695 | 0.969283 |
global S3Connection
if S3Connection != None:
settings = oz.settings
s3_bucket = s3_bucket or settings["s3_bucket"]
opts = {}
if settings["s3_host"]:
opts["host"] = settings["s3_host"]
if settings["aws_access_key"] and settings["aws_secret_key"]:
... | def get_bucket(s3_bucket=None, validate=False) | Gets a bucket from specified settings | 2.62414 | 2.518389 | 1.041991 |
bucket_name = s3_bucket or oz.settings["s3_bucket"]
if bucket_name:
bucket = get_bucket(bucket_name)
key = bucket.get_key(path)
if not key:
key = bucket.new_key(path)
return S3File(key)
else:
return LocalFile(oz.settings["static_path"], path) | def get_file(path, s3_bucket=None) | Gets a file | 3.019249 | 3.170326 | 0.952347 |
new_full_path = os.path.join(self.static_path, new_path)
if replace or not os.path.exists(new_full_path):
shutil.copy2(self.full_path, new_full_path)
return True
return False | def copy(self, new_path, replace=False) | Uses shutil to copy a file over | 2.339736 | 2.164829 | 1.080795 |
if replace or not get_file(new_path).exists():
self.key.copy(self.key.bucket, new_path)
return True
return False | def copy(self, new_path, replace=False) | Uses boto to copy the file to the new path instead of uploading another file to the new key | 5.487185 | 4.398907 | 1.247397 |
global _cached_connection
settings = oz.settings
if settings["redis_cache_connections"] and _cached_connection != None:
return _cached_connection
else:
conn = redis.StrictRedis(
host=settings["redis_host"],
port=settings["redis_port"],
db=settin... | def create_connection() | Sets up a redis configuration | 1.979787 | 1.884429 | 1.050603 |
hit_miss_index = 0
cluster_id_index = otu_id_field
seq_label_index = 8
otus = {}
unassigned_seqs = []
for line in uc_lines:
# skip empty, comment lines
if line.startswith('#') or len(line.strip()) == 0:
continue
curr_line = line.split('\t')
i... | def clusters_from_blast_uc_file(uc_lines, otu_id_field=1) | Parses out hit/miss sequences from usearch blast uc file
All lines should be 'H'it or 'N'o hit. Returns a dict of OTU ids: sequence
labels of the hits, and a list of all sequence labels that miss.
uc_lines = open file object of uc file
otu_id_field: uc field to use as the otu id. 1 is usearch's Clus... | 2.60502 | 2.417358 | 1.077631 |
if not output_filepath:
_, output_filepath = mkstemp(prefix='usearch_fasta_sort',
suffix='.fasta')
log_filepath = join(working_dir, log_name)
params = {}
app = Usearch(params, WorkingDir=working_dir, HALT_EXEC=HALT_EXEC)
data = {'--mergesort': fa... | def usearch_fasta_sort_from_filepath(
fasta_filepath,
output_filepath=None,
log_name="sortlen.log",
HALT_EXEC=False,
save_intermediate_files=False,
remove_usearch_logs=False,
working_dir=None) | Generates sorted fasta file via usearch --mergesort.
fasta_filepath: filepath to input fasta file
output_filepath: filepath for output sorted fasta file.
log_name: string to specify log filename
HALT_EXEC: Used for debugging app controller
save_intermediate_files: Preserve all intermediate files cr... | 3.578749 | 3.461047 | 1.034008 |
if not output_filepath:
_, output_filepath = mkstemp(prefix='usearch_abundance_sorted',
suffix='.fasta')
log_filepath = join(
working_dir,
"minsize_" + str(minsize) + "_" + log_name)
params = {}
app = Usearch(params, WorkingDir=working... | def usearch_sort_by_abundance(
fasta_filepath,
output_filepath=None,
sizein=True,
sizeout=True,
minsize=0,
log_name="abundance_sort.log",
usersort=False,
HALT_EXEC=False,
save_intermediate_files=False,
remove_usearch_logs=False,
wor... | Sorts fasta file by abundance
fasta_filepath = input fasta file, generally a dereplicated fasta
output_filepath = output abundance sorted fasta filepath
sizein = not defined in usearch helpstring
sizeout = not defined in usearch helpstring
minsize = minimum size of cluster to retain.
log_name =... | 4.309338 | 4.565775 | 0.943835 |
if not output_filepath:
_, output_filepath = mkstemp(prefix='usearch_cluster_err_corrected',
suffix='.fasta')
log_filepath = join(working_dir, log_name)
params = {'--sizein': sizein,
'--sizeout': sizeout,
'--id': percent_id_err,... | def usearch_cluster_error_correction(
fasta_filepath,
output_filepath=None,
output_uc_filepath=None,
percent_id_err=0.97,
sizein=True,
sizeout=True,
w=64,
slots=16769023,
maxrejects=64,
log_name="usearch_cluster_err_corrected.log",
... | Cluster for err. correction at percent_id_err, output consensus fasta
fasta_filepath = input fasta file, generally a dereplicated fasta
output_filepath = output error corrected fasta filepath
percent_id_err = minimum identity percent.
sizein = not defined in usearch helpstring
sizeout = not defined... | 2.651961 | 2.77383 | 0.956065 |
if not output_chimera_filepath:
_, output_chimera_filepath = mkstemp(prefix='uchime_chimeras_',
suffix='.fasta')
if not output_non_chimera_filepath:
_, output_non_chimera_filepath = mkstemp(prefix='uchime_non_chimeras_',
... | def usearch_chimera_filter_de_novo(
fasta_filepath,
output_chimera_filepath=None,
output_non_chimera_filepath=None,
abundance_skew=2.0,
log_name="uchime_de_novo_chimera_filtering.log",
usersort=False,
HALT_EXEC=False,
save_intermediate_files=False,
... | Chimera filter de novo, output chimeras and non-chimeras to fastas
fasta_filepath = input fasta file, generally a dereplicated fasta
output_chimera_filepath = output chimera filepath
output_non_chimera_filepath = output non chimera filepath
abundance_skew = abundance skew setting for de novo filtering.... | 2.367947 | 2.385673 | 0.99257 |
output_fp = open(output_concat_filepath, "w")
for label, seq in parse_fasta(open(output_fna_clustered, "U")):
output_fp.write(">%s\n%s\n" % (label, seq))
for label, seq in parse_fasta(open(output_fna_failures, "U")):
output_fp.write(">%s\n%s\n" % (label, seq))
return output_conca... | def concatenate_fastas(output_fna_clustered,
output_fna_failures,
output_concat_filepath) | Concatenates two input fastas, writes to output_concat_filepath
output_fna_clustered: fasta of successful ref clusters
output_fna_failures: de novo fasta of cluster failures
output_concat_filepath: path to write combined fastas to | 1.803838 | 1.844805 | 0.977793 |
fasta_i = open(fasta_filepath, "U")
if not output_filepath:
_, output_filepath = mkstemp(prefix='enumerated_seqs_',
suffix='.fasta')
fasta_o = open(output_filepath, "w")
for label, seq in parse_fasta(fasta_i):
curr_label = ">" + label_prefix ... | def enumerate_otus(fasta_filepath,
output_filepath=None,
label_prefix="",
label_suffix="",
retain_label_as_comment=False,
count_start=0) | Writes unique, sequential count to OTUs
fasta_filepath = input fasta filepath
output_filepath = output fasta filepath
label_prefix = string to place before enumeration
label_suffix = string to place after enumeration
retain_label_as_comment = if True, will place existing label in sequence
comm... | 2.380969 | 2.351099 | 1.012705 |
hit_type_index = 0
seq_label_index = 8
target_label_index = 9
labels_hits = {}
labels_to_keep = []
for line in open(uc_filepath, "U"):
if line.startswith("#") or len(line.strip()) == 0:
continue
curr_line = line.split('\t')
if curr_line[0] == hit_type:... | def get_fasta_from_uc_file(fasta_filepath,
uc_filepath,
hit_type="H",
output_fna_filepath=None,
label_prefix="",
output_dir=None) | writes fasta of sequences from uc file of type hit_type
fasta_filepath: Filepath of original query fasta file
uc_filepath: Filepath of .uc file created by usearch post error filtering
hit_type: type to read from first field of .uc file, "H" for hits, "N" for
no hits.
output_fna_filepath = fasta ... | 2.131449 | 2.153502 | 0.989759 |
de_novo_non_chimeras = []
reference_non_chimeras = []
de_novo_nonchimeras_f = open(output_fp_de_novo_nonchimeras, "U")
reference_nonchimeras_f = open(output_fp_ref_nonchimeras, "U")
output_combined_f = open(output_combined_fp, "w")
for label, seq in parse_fasta(de_novo_nonchimeras_f):
... | def get_retained_chimeras(output_fp_de_novo_nonchimeras,
output_fp_ref_nonchimeras,
output_combined_fp,
chimeras_retention='union') | Gets union or intersection of two supplied fasta files
output_fp_de_novo_nonchimeras: filepath of nonchimeras from de novo
usearch detection.
output_fp_ref_nonchimeras: filepath of nonchimeras from reference based
usearch detection.
output_combined_fp: filepath to write retained sequences to.
... | 1.393223 | 1.403234 | 0.992865 |
# Not sure if I feel confortable using blast as a way to recapitulate
# original read ids....
if not output_filepath:
_, output_filepath = mkstemp(prefix='assign_reads_to_otus',
suffix='.uc')
log_filepath = join(working_dir, log_name)
params = {'-... | def assign_reads_to_otus(original_fasta,
filtered_fasta,
output_filepath=None,
log_name="assign_reads_to_otus.log",
perc_id_blast=0.97,
global_alignment=True,
HALT_EXEC=F... | Uses original fasta file, blasts to assign reads to filtered fasta
original_fasta = filepath to original query fasta
filtered_fasta = filepath to enumerated, filtered fasta
output_filepath = output path to clusters (uc) file
log_name = string specifying output log name
perc_id_blast = percent ID fo... | 4.294404 | 3.83967 | 1.11843 |
if not output_fna_filepath:
_, output_fna_filepath = mkstemp(prefix='abundance_sorted',
suffix='.fna')
if not output_uc_filepath:
_, output_uc_filepath = mkstemp(prefix='abundance_sorted',
suffix='.uc')
... | def sort_by_abundance_usearch61(seq_path,
output_dir='.',
rev=False,
minlen=64,
remove_usearch_logs=False,
HALT_EXEC=False,
outp... | usearch61 application call to sort fasta file by abundance.
seq_path: fasta filepath to be clustered with usearch61
output_dir: directory to output log, OTU mapping, and intermediate files
rev: enable reverse strand matching for clustering/sorting
minlen: minimum sequence length
remove_usearch_log... | 2.436877 | 2.502733 | 0.973686 |
if not output_fna_filepath:
_, output_fna_filepath = mkstemp(prefix='length_sorted', suffix='.fna')
log_filepath = join(output_dir, log_name)
params = {'--minseqlength': minlen,
'--sortbylength': seq_path,
'--output': output_fna_filepath
}
if not... | def sort_by_length_usearch61(seq_path,
output_dir=".",
minlen=64,
remove_usearch_logs=False,
HALT_EXEC=False,
output_fna_filepath=None,
log_name="... | usearch61 application call to sort fasta file by length.
seq_path: fasta filepath to be clustered with usearch61
output_dir: directory to output log, OTU mapping, and intermediate files
minlen: minimum sequence length
remove_usearch_logs: Saves usearch log files
HALT_EXEC: application controller o... | 2.75788 | 2.832429 | 0.97368 |
log_filepath = join(output_dir, log_filepath)
params = {
'--usearch_global': intermediate_fasta,
'--db': refseqs_fp,
'--minseqlength': minlen,
'--id': percent_id,
'--uc': output_uc_filepath,
'--wordlength': wordlength,
'--maxrejects': usearch61_maxr... | def usearch61_cluster_ref(intermediate_fasta,
refseqs_fp,
percent_id=0.97,
rev=False,
minlen=64,
output_dir=".",
remove_usearch_logs=False,
... | Cluster input fasta seqs against reference database
seq_path: fasta filepath to be clustered with usearch61
refseqs_fp: reference fasta filepath, used to cluster sequences against.
percent_id: percentage id to cluster at
rev: enable reverse strand matching for clustering
minlen: minimum sequence ... | 2.280444 | 2.5387 | 0.898273 |
log_filepath = join(output_dir, log_name)
params = {'--minseqlength': minlen,
'--cluster_fast': intermediate_fasta,
'--id': percent_id,
'--uc': output_uc_filepath,
'--wordlength': wordlength,
'--maxrejects': usearch61_maxrejects,
... | def usearch61_fast_cluster(intermediate_fasta,
percent_id=0.97,
minlen=64,
output_dir=".",
remove_usearch_logs=False,
wordlength=8,
usearch61_maxrejects=8,
... | Performs usearch61 de novo fast clustering via cluster_fast option
Only supposed to be used with length sorted data (and performs length
sorting automatically) and does not support reverse strand matching
intermediate_fasta: fasta filepath to be clustered with usearch61
percent_id: percentage id to ... | 2.710952 | 2.870152 | 0.944533 |
log_filepath = join(output_dir, log_name)
params = {'--minseqlength': minlen,
'--cluster_smallmem': intermediate_fasta,
'--id': percent_id,
'--uc': output_uc_filepath,
'--wordlength': wordlength,
'--maxrejects': usearch61_maxrejects,
... | def usearch61_smallmem_cluster(intermediate_fasta,
percent_id=0.97,
minlen=64,
rev=False,
output_dir=".",
remove_usearch_logs=False,
w... | Performs usearch61 de novo clustering via cluster_smallmem option
Only supposed to be used with length sorted data (and performs length
sorting automatically) and does not support reverse strand matching
intermediate_fasta: fasta filepath to be clustered with usearch61
percent_id: percentage id to c... | 2.480011 | 2.45741 | 1.009197 |
params = {'--minseqlength': minlen,
'--uchime_denovo': abundance_fp,
'--uchimeout': uchime_denovo_fp,
'--minh': usearch61_minh,
'--xn': usearch61_xn,
'--dn': usearch61_dn,
'--mindiffs': usearch61_mindiffs,
'--min... | def usearch61_chimera_check_denovo(abundance_fp,
uchime_denovo_fp,
minlen=64,
output_dir=".",
remove_usearch_logs=False,
uchime_denovo_log_fp="uc... | Does de novo, abundance based chimera checking with usearch61
abundance_fp: input consensus fasta file with abundance information for
each cluster.
uchime_denovo_fp: output uchime file for chimera results.
minlen: minimum sequence length for usearch input fasta seqs.
output_dir: output directory
... | 2.044831 | 2.088498 | 0.979092 |
params = {'--minseqlength': minlen,
'--uchime_ref': abundance_fp,
'--uchimeout': uchime_ref_fp,
'--db': reference_seqs_fp,
'--minh': usearch61_minh,
'--xn': usearch61_xn,
'--dn': usearch61_dn,
'--mindiffs': usear... | def usearch61_chimera_check_ref(abundance_fp,
uchime_ref_fp,
reference_seqs_fp,
minlen=64,
output_dir=".",
remove_usearch_logs=False,
... | Does reference based chimera checking with usearch61
abundance_fp: input consensus fasta file with abundance information for
each cluster.
uchime_ref_fp: output uchime filepath for reference results
reference_seqs_fp: reference fasta database for chimera checking.
minlen: minimum sequence length f... | 2.59231 | 2.670927 | 0.970566 |
dereplicated_clusters = {}
seed_hit_ix = 0
seq_id_ix = 8
seed_id_ix = 9
for line in dereplicated_uc_lines:
if line.startswith("#") or len(line.strip()) == 0:
continue
curr_line = line.strip().split('\t')
if curr_line[seed_hit_ix] == "S":
derepl... | def parse_dereplicated_uc(dereplicated_uc_lines) | Return dict of seq ID:dereplicated seq IDs from dereplicated .uc lines
dereplicated_uc_lines: list of lines of .uc file from dereplicated seqs from
usearch61 (i.e. open file of abundance sorted .uc data) | 2.3831 | 2.380971 | 1.000894 |
clusters = {}
failures = []
seed_hit_ix = 0
otu_id_ix = 1
seq_id_ix = 8
ref_id_ix = 9
for line in clustered_uc_lines:
if line.startswith("#") or len(line.strip()) == 0:
continue
curr_line = line.strip().split('\t')
if curr_line[seed_hit_ix] == "S":... | def parse_usearch61_clusters(clustered_uc_lines,
otu_prefix='denovo',
ref_clustered=False) | Returns dict of cluster ID:seq IDs
clustered_uc_lines: lines from .uc file resulting from de novo clustering
otu_prefix: string added to beginning of OTU ID.
ref_clustered: If True, will attempt to create dict keys for clusters as
they are read from the .uc file, rather than from seed lines. | 2.3088 | 2.236177 | 1.032477 |
clusters = {}
for curr_denovo_key in de_novo_clusters.keys():
clusters[curr_denovo_key] = de_novo_clusters[curr_denovo_key]
curr_clusters = []
for curr_denovo_id in de_novo_clusters[curr_denovo_key]:
curr_clusters += dereplicated_clusters[curr_denovo_id]
cluste... | def merge_clusters_dereplicated_seqs(de_novo_clusters,
dereplicated_clusters) | combines de novo clusters and dereplicated seqs to OTU id:seqs dict
de_novo_clusters: dict of OTU ID:clustered sequences
dereplicated_clusters: dict of seq IDs: dereplicated seq IDs | 2.018526 | 2.067259 | 0.976426 |
curr_failures = set(failures)
dereplicated_ids = set(dereplicated_clusters)
for curr_failure in curr_failures:
if curr_failure in dereplicated_ids:
failures += dereplicated_clusters[curr_failure]
return failures | def merge_failures_dereplicated_seqs(failures,
dereplicated_clusters) | Appends failures from dereplicated seqs to failures list
failures: list of failures
dereplicated_clusters: dict of seq IDs: dereplicated seq IDs | 3.109963 | 2.816657 | 1.104133 |
parsed_out = open(output_fasta_fp, "w")
for label, seq in parse_fasta(open(seq_path), "U"):
curr_label = label.split()[0]
if curr_label in failures:
parsed_out.write(">%s\n%s\n" % (label, seq))
parsed_out.close()
return output_fasta_fp | def parse_usearch61_failures(seq_path,
failures,
output_fasta_fp) | Parses seq IDs from failures list, writes to output_fasta_fp
seq_path: filepath of original input fasta file.
failures: list/set of failure seq IDs
output_fasta_fp: path to write parsed sequences | 2.737001 | 2.961669 | 0.924141 |
if oz.settings.get('debug'):
exception_type, exception_value, tback = sys.exc_info()
is_breakpoint = isinstance(exception_value, oz.error_pages.DebugBreakException)
frames = oz.error_pages.get_frames(tback, is_breakpoint)
frames.reverse()
i... | def _on_error_page_write_error(self, status_code, **kwargs) | Replaces the default Tornado error page with a Django-styled one | 4.178675 | 4.004932 | 1.043382 |
value = self.get_cookie(name)
if value != None:
self.clear_cookie(name)
return escape.url_unescape(value) | def get_blink_cookie(self, name) | Gets a blink cookie value | 4.254957 | 4.154637 | 1.024146 |
self.set_cookie("blink_message", escape.url_escape(message), httponly=True)
self.set_cookie("blink_type", escape.url_escape(type), httponly=True) | def set_blink(self, message, type="info") | Sets the blink, a one-time transactional message that is shown on the
next page load | 2.973532 | 3.103211 | 0.958212 |
# keys are not remapped. Tested against seq_ids of 100char length
seqs = SequenceCollection(seqs, MolType=moltype)
#Create mapping between abbreviated IDs and full IDs
int_map, int_keys = seqs.getIntMap()
#Create SequenceCollection from int_map.
int_map = SequenceCollection(int_map,MolType=... | def cdhit_clusters_from_seqs(seqs, moltype=DNA, params=None) | Returns the CD-HIT clusters given seqs
seqs : dict like collection of sequences
moltype : cogent.core.moltype object
params : cd-hit parameters
NOTE: This method will call CD_HIT if moltype is PROTIEN,
CD_HIT_EST if moltype is RNA/DNA, and raise if any other
moltype is ... | 4.831007 | 4.534359 | 1.065422 |
# keys are not remapped. Tested against seq_ids of 100char length
seqs = SequenceCollection(seqs, MolType=moltype)
# setup params and make sure the output argument is set
if params is None:
params = {}
if '-o' not in params:
_, params['-o'] = mkstemp()
# call the correct v... | def cdhit_from_seqs(seqs, moltype, params=None) | Returns the CD-HIT results given seqs
seqs : dict like collection of sequences
moltype : cogent.core.moltype object
params : cd-hit parameters
NOTE: This method will call CD_HIT if moltype is PROTIEN,
CD_HIT_EST if moltype is RNA/DNA, and raise if any other
moltype is passed. | 4.98029 | 4.546582 | 1.095392 |
clusters = []
curr_cluster = []
for l in lines:
if l.startswith('>Cluster'):
if not curr_cluster:
continue
clusters.append(curr_cluster)
curr_cluster = []
else:
curr_cluster.append(clean_cluster_seq_id(l.split()[2]))
... | def parse_cdhit_clstr_file(lines) | Returns a list of list of sequence ids representing clusters | 2.393203 | 2.249152 | 1.064047 |
if data:
self.Parameters['-i']\
.on(super(CD_HIT,self)._input_as_multiline_string(data))
return '' | def _input_as_multiline_string(self, data) | Writes data to tempfile and sets -i parameter
data -- list of lines | 17.162863 | 12.525588 | 1.370224 |
if data:
self.Parameters['-i']\
.on(super(CD_HIT,self)._input_as_lines(data))
return '' | def _input_as_lines(self, data) | Writes data to tempfile and sets -i parameter
data -- list of lines, ready to be written to file | 20.903145 | 14.729444 | 1.41914 |
if self.Parameters['-o'].isOn():
return ''.join([self.Parameters['-o'].Value, '.clstr'])
else:
raise ValueError, "No output file specified" | def _get_clstr_outfile(self) | Returns the absolute path to the clstr outfile | 5.741837 | 4.82235 | 1.190672 |
result = {}
result['FASTA'] = ResultPath(Path=self._get_seqs_outfile())
result['CLSTR'] = ResultPath(Path=self._get_clstr_outfile())
return result | def _get_result_paths(self, data) | Return dict of {key: ResultPath} | 7.039823 | 5.394265 | 1.305057 |
look_ahead = LookAhead(tokens)
segments = Segment()
while not look_ahead.empty():
if look_ahead.peek().type not in self.whitespace: # Paragraph!
paragraph = MatchableSegment(look_ahead.i)
while not look_ahead.empty() and \
... | def segment(self, tokens) | Segments a sequence of tokens into a sequence of segments.
:Parameters:
tokens : `list` ( :class:`~deltas.Token` ) | 2.68816 | 2.79005 | 0.963481 |
# we only use one conn at a time currently but we may as well do this...
created_conn = False
while not created_conn:
if len(self.conns) == 0:
self.conns.append(PushConnection(self, self.address, self.certfile, self.keyfile))
created_conn = T... | def send(self, payload, token, expiration=None, priority=None, identifier=None) | Attempts to send a push message. On network failures, progagates the exception.
It is advised to make all text in the payload dictionary unicode objects and not
mix unicode objects and str objects. If str objects are used, they must be
in UTF-8 encoding.
Args:
payload (dict):... | 3.963712 | 4.24784 | 0.933112 |
if not self.fbaddress:
raise Exception("Attempted to fetch feedback but no feedback_address supplied")
fbconn = FeedbackConnection(self, self.fbaddress, self.certfile, self.keyfile)
return fbconn.get_all() | def get_all_feedback(self) | Connects to the feedback service and returns any feedback that is sent
as a list of FeedbackItem objects.
Blocks the current greenlet until all feedback is returned.
If a network error occurs before any feedback is received, it is
propagated to the caller. Otherwise, it is ignored and ... | 6.981668 | 7.04724 | 0.990695 |
if response.startswith('\n'):
response = response[1:]
tree = etree.fromstring(response)
return tree | def _parse_xml(self, response) | Run our XML parser (lxml in this case) over our response text. Lxml
doesn't enjoy having xml/encoding information in the header so we strip
that out if necessary. We return a parsed XML object that can be
used by the calling API method and massaged into a more appropriate
format. | 5.308011 | 4.272117 | 1.242478 |
status_code = error.response.status_code
message = error.message
if 403 == status_code:
raise NewRelicInvalidApiKeyException(message)
elif 404 == status_code:
raise NewRelicUnknownApplicationException(message)
elif 422 == status_code:
... | def _handle_api_error(self, error) | New Relic cheerfully provides expected API error codes depending on your
API call deficiencies so we convert these to exceptions and raise them
for the user to handle as they see fit. | 2.643079 | 2.245408 | 1.177104 |
current = datetime.datetime.now()
try:
previous = getattr(self, api_call.__name__ + "_window")
# Force the calling of our property so we can
# handle not having set it yet.
previous.__str__
except AttributeError:
now = datetime... | def _api_rate_limit_exceeded(self, api_call, window=60) | We want to keep track of the last time we sent a request to the NewRelic
API, but only for certain operations. This method will dynamically add
an attribute to the Client class with a unix timestamp with the name of
the API api_call we make so that we can check it later. We return the
a... | 4.859827 | 4.420214 | 1.099455 |
endpoint = "https://rpm.newrelic.com"
uri = "{endpoint}/accounts/{id}/applications.xml".format(endpoint=endpoint, id=self.account_id)
response = self._make_get_request(uri)
applications = []
for application in response.findall('.//application'):
application_... | def view_applications(self) | Requires: account ID (taken from Client object)
Returns: a list of Application objects
Endpoint: rpm.newrelic.com
Errors: 403 Invalid API Key
Method: Get | 3.249606 | 2.53195 | 1.28344 |
endpoint = "https://api.newrelic.com"
uri = "{endpoint}/api/v1/accounts/{account_id}/applications/delete.xml"\
.format(endpoint=endpoint, account_id=self.account_id)
payload = applications
response = self._make_post_request(uri, payload)
failed_deletions = ... | def delete_applications(self, applications) | Requires: account ID, application ID (or name).
Input should be a dictionary { 'app_id': 1234 , 'app': 'My Application'}
Returns: list of failed deletions (if any)
Endpoint: api.newrelic.com
Errors: None Explicit, failed deletions will be in XML
Method: Post | 3.770535 | 3.137919 | 1.201604 |
endpoint = "https://rpm.newrelic.com"
uri = "{endpoint}/deployments.xml".format(endpoint=endpoint)
deploy_event = {}
if not application_id is None:
deploy_event['deployment[application_id]'] = application_id
elif not application_name is None:
d... | def notify_deployment(self, application_id=None, application_name=None, description=None, revision=None, changelog=None, user=None) | Notify NewRelic of a deployment.
http://newrelic.github.io/newrelic_api/NewRelicApi/Deployment.html
:param description:
:param revision:
:param changelog:
:param user:
:return: A dictionary containing all of the returned keys from the API | 2.069964 | 2.012023 | 1.028797 |
# Make sure we play it slow
self._api_rate_limit_exceeded(self.get_metric_names)
# Construct our GET request parameters into a nice dictionary
parameters = {'re': re, 'limit': limit}
endpoint = "https://api.newrelic.com"
uri = "{endpoint}/api/v1/applications/{a... | def get_metric_names(self, agent_id, re=None, limit=5000) | Requires: application ID
Optional: Regex to filter metric names, limit of results
Returns: A dictionary,
key: metric name,
value: list of fields available for a given metric
Method: Get
Restrictions: Rate limit to 1x per minute
Errors: 403... | 6.556716 | 6.534612 | 1.003383 |
# TODO: it may be nice to have some helper methods that make it easier
# to query by common time frames based off the time period folding
# of the metrics returned by the New Relic API.
# Make sure we aren't going to hit an API timeout
self._api_rate_limit_e... | def get_metric_data(self, applications, metrics, field, begin, end, summary=False) | Requires: account ID,
list of application IDs,
list of metrics,
metric fields,
begin,
end
Method: Get
Endpoint: api.newrelic.com
Restrictions: Rate limit to 1x per minute
Errors: 403 Invalid API key... | 5.695838 | 5.585226 | 1.019804 |
endpoint = "https://rpm.newrelic.com"
remote_file = "threshold_values.xml"
uri = "{endpoint}/accounts/{account_id}/applications/{app_id}/{xml}".format(endpoint=endpoint, account_id=self.account_id, app_id=application_id, xml=remote_file)
response = self._make_get_request(uri)
... | def get_threshold_values(self, application_id) | Requires: account ID, list of application ID
Method: Get
Endpoint: api.newrelic.com
Restrictions: ???
Errors: 403 Invalid API key, 422 Invalid Parameters
Returns: A list of threshold_value objects, each will have information
about its start/end time, metric name,... | 4.122794 | 3.96375 | 1.040125 |
endpoint = "https://api.newrelic.com"
uri = "{endpoint}/api/v1/accounts/{id}/servers.xml".format(endpoint=endpoint, id=self.account_id)
response = self._make_get_request(uri)
servers = []
for server in response.findall('.//server'):
server_properties = {}
... | def view_servers(self) | Requires: account ID (taken from Client object)
Returns: a list of Server objects
Endpoint: api.newrelic.com
Errors: 403 Invalid API Key
Method: Get | 3.035821 | 2.644729 | 1.147876 |
endpoint = "https://api.newrelic.com"
uri = "{endpoint}/api/v1/accounts/{account_id}/servers/{server_id}.xml".format(
endpoint=endpoint,
account_id=self.account_id,
server_id=server_id)
response = self._make_delete_request(uri)
failed_deletion... | def delete_servers(self, server_id) | Requires: account ID, server ID
Input should be server id
Returns: list of failed deletions (if any)
Endpoint: api.newrelic.com
Errors: 403 Invalid API Key
Method: Delete | 2.996866 | 2.514813 | 1.191686 |
abs_r1_path = os.path.abspath(reads1_infile_path)
abs_r2_path = os.path.abspath(reads2_infile_path)
infile_paths = [abs_r1_path, abs_r2_path]
# check / make absolute infile paths
for p in infile_paths:
if not os.path.exists(p):
raise IOError('File not found at: %s' % p)
... | def join_paired_end_reads_fastqjoin(
reads1_infile_path,
reads2_infile_path,
perc_max_diff=None, # typical default is 8
min_overlap=None, # typical default is 6
outfile_label='fastqjoin',
params={},
working_dir=tempfile.gettempdir(),
SuppressStderr=True,... | Runs fastq-join, with default parameters to assemble paired-end reads.
Returns file path string.
-reads1_infile_path : reads1.fastq infile path
-reads2_infile_path : reads2.fastq infile path
-perc_max_diff : maximum % diff of overlap differences allowed
-min_overlap : minimum al... | 2.721765 | 2.717186 | 1.001685 |
if self.Parameters['-o'].isOn():
output_path = self._absolute(str(self.Parameters['-o'].Value))
else:
raise ValueError("No output path specified.")
return output_path | def _get_output_path(self) | Checks if a base file label / path is set. Returns absolute path. | 6.079585 | 4.926566 | 1.234041 |
if self.Parameters['-r'].isOn():
stitch_path = self._absolute(str(self.Parameters['-r'].Value))
return stitch_path
elif self.Parameters['-r'].isOff():
return None | def _get_stitch_report_path(self) | Checks if stitch report label / path is set. Returns absolute path. | 5.265127 | 4.338033 | 1.213713 |
output_path = self._get_output_path()
result = {}
# always output:
result['Assembled'] = ResultPath(Path=output_path + 'join',
IsWritten=True)
result['UnassembledReads1'] = ResultPath(Path=output_path + 'un1',
... | def _get_result_paths(self, data) | Capture fastq-join output.
Three output files are produced, in the form of
outputjoin : assembled paired reads
outputun1 : unassembled reads_1
outputun2 : unassembled reads_2
If a barcode / mate-pairs file is also provided then the following
additional files... | 3.180452 | 2.730983 | 1.164582 |
'''
Given a list of fields (or several other variants of the same),
return back a consistent, normalized form of the same.
To forms are currently supported:
dictionary form: dict 'key' is the field name
and dict 'value' is either 1 (include)
... | def parse_fields(fields, as_dict=False) | Given a list of fields (or several other variants of the same),
return back a consistent, normalized form of the same.
To forms are currently supported:
dictionary form: dict 'key' is the field name
and dict 'value' is either 1 (include)
... | 6.144442 | 1.745612 | 3.519936 |
'''
Return back start and end dates given date string
:param date: metrique date (range) to apply to pql query
The tilde '~' symbol is used as a date range separated.
A tilde by itself will mean 'all dates ranges possible'
and will therefore search all objects irrelevant of it's
_end date... | def date_range(date, func='date') | Return back start and end dates given date string
:param date: metrique date (range) to apply to pql query
The tilde '~' symbol is used as a date range separated.
A tilde by itself will mean 'all dates ranges possible'
and will therefore search all objects irrelevant of it's
_end date timestamp.
... | 6.074894 | 2.66265 | 2.281522 |
'''
Given a SQLAlchemy Table() instance, generate a SQLAlchemy
Query() instance with the given parameters.
:param table: SQLAlchemy Table() instance
:param query: MQL query
:param date: metrique date range query
:param date: metrique date range query element
:param fields: list of field... | def parse(table, query=None, date=None, fields=None,
distinct=False, limit=None, alias=None) | Given a SQLAlchemy Table() instance, generate a SQLAlchemy
Query() instance with the given parameters.
:param table: SQLAlchemy Table() instance
:param query: MQL query
:param date: metrique date range query
:param date: metrique date range query element
:param fields: list of field names to re... | 4.358181 | 2.904865 | 1.500304 |
'''
Enqueue an arbitrary synchronous function.
Deprecated: Use async version instead
'''
worker = self.pick_sticky(0) # just pick first always
args = (func,) + func_args
coro = worker.enqueue(enums.Task.FUNC, args)
asyncio.ensure_future(coro) | def enqueue_sync(self, func, *func_args) | Enqueue an arbitrary synchronous function.
Deprecated: Use async version instead | 12.292195 | 8.956233 | 1.372474 |
'''
Enqueue an arbitrary synchronous function.
'''
worker = self.pick_sticky(0) # just pick first always
args = (func,) + func_args
await worker.enqueue(enums.Task.FUNC, args) | async def async_enqueue_sync(self, func, *func_args) | Enqueue an arbitrary synchronous function. | 16.419867 | 14.146173 | 1.160728 |
'''
Enqueue the download of the given foreign resource.
Deprecated: Use async version instead
'''
worker = self.pick_sticky(resource.url_string)
coro = worker.enqueue(enums.Task.DOWNLOAD, (resource,))
asyncio.ensure_future(coro) | def enqueue_download(self, resource) | Enqueue the download of the given foreign resource.
Deprecated: Use async version instead | 15.359205 | 8.421374 | 1.823836 |
'''
Enqueue the download of the given foreign resource.
'''
worker = self.pick_sticky(resource.url_string)
await worker.enqueue(enums.Task.DOWNLOAD, (resource,)) | async def async_enqueue_download(self, resource) | Enqueue the download of the given foreign resource. | 19.291233 | 13.049448 | 1.478318 |
'''
Enqueue use of the given converter to convert to given
resources.
Deprecated: Use async version instead
'''
worker = self.pick_sticky(from_resource.url_string)
args = (converter, from_resource, to_resource)
coro = worker.enqueue(enums.Task.CONVERT, ar... | def enqueue_convert(self, converter, from_resource, to_resource) | Enqueue use of the given converter to convert to given
resources.
Deprecated: Use async version instead | 10.097931 | 5.383 | 1.875893 |
'''
Enqueue use of the given converter to convert to given
from and to resources.
'''
worker = self.pick_sticky(from_.url_string)
args = (converter, from_, to)
await worker.enqueue(enums.Task.CONVERT, args) | async def async_enqueue_convert(self, converter, from_, to) | Enqueue use of the given converter to convert to given
from and to resources. | 15.685034 | 7.942734 | 1.974765 |
'''
Enqueue a multi-step conversion process, from the given URL string
(which is assumed to have been downloaded / resolved)
'''
worker = self.pick_sticky(url_string)
args = (url_string, to_type)
await worker.enqueue(enums.Task.MULTICONVERT, args) | async def async_enqueue_multiconvert(self, url_string, to_type) | Enqueue a multi-step conversion process, from the given URL string
(which is assumed to have been downloaded / resolved) | 11.218478 | 5.017177 | 2.236014 |
'''
Returns the in-plane strain assuming no lattice relaxation, which
is positive for tensile strain and negative for compressive strain.
'''
if self._strain_out_of_plane is not None:
return ((self._strain_out_of_plane / -2.) *
(self.unstrained.c11... | def strain_in_plane(self, **kwargs) | Returns the in-plane strain assuming no lattice relaxation, which
is positive for tensile strain and negative for compressive strain. | 6.237008 | 3.889457 | 1.603568 |
'''
Returns the out-of-plane strain assuming no lattice relaxation, which
is negative for tensile strain and positive for compressive strain.
This is the strain measured by X-ray diffraction (XRD) symmetric
omega-2theta scans.
'''
if self._strain_out_of_plane is n... | def strain_out_of_plane(self, **kwargs) | Returns the out-of-plane strain assuming no lattice relaxation, which
is negative for tensile strain and positive for compressive strain.
This is the strain measured by X-ray diffraction (XRD) symmetric
omega-2theta scans. | 7.344341 | 2.550884 | 2.879135 |
'''
Returns the substrate's lattice parameter.
'''
if self.substrate is not None:
return self.substrate.a(**kwargs)
else:
return (self.unstrained.a(**kwargs) /
(1. - self.strain_in_plane(**kwargs))) | def substrate_a(self, **kwargs) | Returns the substrate's lattice parameter. | 5.577683 | 3.932504 | 1.418354 |
'''
Returns the strain-shifted conduction band offset (CBO), assuming
the strain affects all conduction band valleys equally.
'''
return self.unstrained.CBO(**kwargs) + self.CBO_strain_shift(**kwargs) | def CBO(self, **kwargs) | Returns the strain-shifted conduction band offset (CBO), assuming
the strain affects all conduction band valleys equally. | 15.172059 | 3.331132 | 4.554626 |
'''
Returns the strain-shifted Gamma-valley conduction band offset (CBO),
assuming the strain affects all conduction band valleys equally.
'''
return (self.unstrained.CBO_Gamma(**kwargs) +
self.CBO_strain_shift(**kwargs)) | def CBO_Gamma(self, **kwargs) | Returns the strain-shifted Gamma-valley conduction band offset (CBO),
assuming the strain affects all conduction band valleys equally. | 14.926068 | 2.943589 | 5.070704 |
'''
Returns the strain-shifted L-valley conduction band offset (CBO),
assuming the strain affects all conduction band valleys equally.
'''
return (self.unstrained.CBO_L(**kwargs) +
self.CBO_strain_shift(**kwargs)) | def CBO_L(self, **kwargs) | Returns the strain-shifted L-valley conduction band offset (CBO),
assuming the strain affects all conduction band valleys equally. | 14.451994 | 2.932606 | 4.928038 |
'''
Returns the strain-shifted X-valley conduction band offset (CBO),
assuming the strain affects all conduction band valleys equally.
'''
return (self.unstrained.CBO_X(**kwargs) +
self.CBO_strain_shift(**kwargs)) | def CBO_X(self, **kwargs) | Returns the strain-shifted X-valley conduction band offset (CBO),
assuming the strain affects all conduction band valleys equally. | 13.609776 | 2.949825 | 4.613757 |
'''
Returns the strain-shifted bandgap, ``Eg``.
'''
return self.unstrained.Eg(**kwargs) + self.Eg_strain_shift(**kwargs) | def Eg(self, **kwargs) | Returns the strain-shifted bandgap, ``Eg``. | 17.915789 | 5.774509 | 3.102565 |
for subsegment_or_token in self:
if isinstance(subsegment_or_token, Segment):
subsegment = subsegment_or_token
for token in subsegment.tokens():
yield token
else:
token = subsegment_or_token
yiel... | def tokens(self) | `generator` : the tokens in this segment | 2.918841 | 2.348529 | 1.242838 |
return_error = { "code": self.get_status() }
exc_info = kwargs.get("exc_info")
if exc_info and isinstance(exc_info[1], oz.json_api.ApiError):
return_error["error"] = exc_info[1].message
else:
return_error["error"] = API_ERROR_CODE_MAP.get(self.get_statu... | def _api_on_write_error(self, status_code, **kwargs) | Catches errors and renders it as a JSON message. Adds the traceback if
debug is enabled. | 4.368847 | 3.764472 | 1.160547 |
# Get the callback argument if JSONP is allowed
callback = self.get_argument("callback", None) if oz.settings["allow_jsonp"] else None
# We're pretty strict with what callback names are allowed, just in case
if callback and not CALLBACK_VALIDATOR.match(callback):
r... | def respond(self, obj) | Gives a response JSON(P) message | 4.839264 | 4.798688 | 1.008456 |
if self._decoded_body == None:
# Try to decode the JSON body. But raise an error if the
# content-type is unexpected, or the JSON is invalid.
raw_content_type = self.request.headers.get("content-type") or ""
content_type = raw_content_type.split(";")[0]... | def body(self) | Gets the JSON body of the request | 3.619978 | 3.371331 | 1.073753 |
return ''.join(map(str,
filter(is_not_None,
[self.Prefix, self.Name]))) | def _get_id(self) | Construct and return the identifier | 16.683102 | 12.430493 | 1.342111 |
if val is False:
raise ParameterError("Turning the ValuedParameter on with value "
"False is the same as turning it off. Use "
"another value.")
elif self.IsPath:
self.Value = FilePath(val)
else:
... | def on(self, val=None) | Turns the MixedParameter ON by setting its Value to val
An attempt to turn the parameter on with value 'False' will result
in an error, since this is the same as turning the parameter off.
Turning the MixedParameter ON without a value or with value 'None'
will let the parameter... | 11.318591 | 7.653682 | 1.478843 |
'''
Return a flat list of absolute paths to all assets required by this
viewer
'''
return sum([
[self.prefix_asset(viewer, relpath) for relpath in viewer.assets]
for viewer in self.viewers
], []) | def get_assets(self) | Return a flat list of absolute paths to all assets required by this
viewer | 8.979395 | 4.736151 | 1.895927 |
'''
Returns a BytesResource to build the viewers JavaScript
'''
# Basename could be used for controlling caching
# basename = 'viewers_%s' % settings.get_cache_string()
node_packages = self.get_node_packages()
# sort_keys is essential to ensure resulting string is... | def get_resource(self) | Returns a BytesResource to build the viewers JavaScript | 9.215097 | 6.361534 | 1.448565 |
parser = ArgumentParser()
subs = parser.add_subparsers(dest='cmd')
setup_parser = subs.add_parser('search')
setup_parser.add_argument('-e', '--engine', dest='engine', required=True,
help='Search engine to use.',
choices=['bing'])
setup... | def main() | Run the core. | 2.405166 | 2.407547 | 0.999011 |
message_id = request.GET.get('messageId')
status_id = request.GET.get('status')
status_msg = NEXMO_STATUSES.get(status_id, UNKNOWN_STATUS)
error_id = int(request.GET.get('err-code'))
error_msg = NEXMO_MESSAGES.get(error_id, UNKNOWN_MESSAGE)
logger.info(u'Nexmo callback: Sms = %s, Status = ... | def callback(request) | Callback URL for Nexmo. | 3.504843 | 3.21893 | 1.088822 |
'''
Utilize hmac module to hash a secret, a string specifying a resource URL,
and a string specifying a target type into a (string) hex digest.
'''
# Normalize and sanitize input resource URL and target type, and then
# convert to bytes
target_type_bytes = str(TypeString(target_type)).encode... | def get_hmac_sha1_digest(secret, resource_url, target_type, api_key=None) | Utilize hmac module to hash a secret, a string specifying a resource URL,
and a string specifying a target type into a (string) hex digest. | 4.109401 | 2.901436 | 1.416334 |
if os.path.exists(DEPLOY_YAML):
_yellow("\nIt looks like you've already gone through the questionnaire.")
cont = prompt("Do you want to go through it again and overwrite the current one?", default="No")
if cont.strip().lower() == "no":
return None
_green("\nWelcome to t... | def init(provider=None) | Runs through a questionnaire to set up your project's deploy settings | 4.006245 | 3.911099 | 1.024327 |
site = init(provider)
if not site:
site = yaml.safe_load(_read_file(DEPLOY_YAML))
provider_class = PROVIDERS[site['provider']]
provider_class.init(site) | def setup(provider=None) | Creates the provider config files needed to deploy your project | 7.739685 | 7.548242 | 1.025363 |
if os.path.exists(DEPLOY_YAML):
site = yaml.safe_load(_read_file(DEPLOY_YAML))
provider_class = PROVIDERS[site['provider']]
provider_class.deploy() | def deploy(provider=None) | Deploys your project | 6.597011 | 6.729646 | 0.980291 |
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