| |
| |
| import os |
|
|
|
|
| def find_missing_info(seed_alignment_dir: str, |
| tree_dir: str): |
| """ |
| find if pfams are missing either tree or MSA seed alignment files |
| |
| inputs: |
| ------- |
| - seed_alignment_dir: contains seed alignments |
| - tree_dir: contains trees |
| |
| returns: |
| -------- |
| """ |
| pfams_in_msas = set( [f.replace('.seed','') for f in os.listdir(seed_alignment_dir) |
| if f.startswith('PF') and f.endswith('.seed')] ) |
| pfams_in_trees = set( [f.replace('.tree','') for f in os.listdir(tree_dir) |
| if f.startswith('PF') and f.endswith('.tree')] ) |
| |
| missing_trees = pfams_in_msas - pfams_in_trees |
| missing_msas = pfams_in_trees - pfams_in_msas |
| return list(missing_trees), list(missing_msas) |
| |
|
|
| def rename_file_in_place(filename: str, |
| in_dir:str, |
| prefix: str): |
| """ |
| rename a file in place |
| |
| inputs: |
| ------- |
| - filename: name of file (usually pfam.seed or pfam.tree) |
| - in_dir: name of folder |
| - prefix: the temporary prefix |
| |
| returns: |
| -------- |
| (None) |
| |
| outputs: |
| -------- |
| - renames file in place |
| """ |
| os.rename(f'./{in_dir}/{prefix}_{filename}', |
| f'./{in_dir}/{filename}') |
|
|
|
|
| def move_file_to_originals(filename: str, |
| in_dir: str): |
| """ |
| move the file from in_dir to in_dir/originals |
| |
| inputs: |
| ------- |
| - filename: name of file (usually pfam.seed or pfam.tree) |
| - in_dir: name of folder |
| |
| returns: |
| -------- |
| (None) |
| |
| outputs: |
| -------- |
| - new directory at {in_dir}/originals |
| """ |
| if filename not in os.listdir(f'{in_dir}/originals'): |
| os.rename(f'./{in_dir}/{filename}', |
| f'./{in_dir}/originals/{filename}') |
|
|
|
|
| def make_sub_folder(in_dir, sub_folder): |
| """ |
| try making a folder inside in_dir |
| |
| inputs: |
| ------- |
| - in_dir: name of directory to contain sub_folder |
| - sub_folder: new sub_folder |
| |
| returns: |
| -------- |
| (None) |
| |
| outputs: |
| -------- |
| - new directory at {in_dir}/{sub_folder} |
| """ |
| if sub_folder not in os.listdir(in_dir): |
| os.mkdir(f'{in_dir}/{sub_folder}') |
|
|
|
|
| def make_orig_folder(in_dir: str): |
| make_sub_folder(in_dir = in_dir, |
| sub_folder = 'originals') |
| |
|
|
| def msa_dimensions(pfam_seed_file: str): |
| """ |
| Open a pfam seed file and count the width and depth |
| |
| Doesn't depend on info in given PFam annotation line, since sequences |
| could be removed during processing |
| |
| inputs: |
| ------- |
| - pfam_seed_file: the single Pfam seed file to split |
| |
| returns: |
| -------- |
| - out_dict: dictionary of MSA dimensions |
| """ |
| pfam_name = pfam_seed_file.split('/')[-1].replace('.seed','') |
| msa_width = -1 |
| num_seqs = 0 |
| with open(pfam_seed_file, 'r', encoding='latin') as f: |
| for line in f: |
| if not line.startswith('#'): |
| num_seqs += 1 |
| |
| if msa_width == -1: |
| msa_width = len( line.strip().split()[-1] ) |
| |
| out_dict = {'name': pfam_name, |
| 'num_seqs': num_seqs, |
| 'msa_width': msa_width} |
| |
| return out_dict |
|
|
|
|
