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Passing loci_finder variable to each function instead of defining it …
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…as global.
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@rfm-targa
rfm-targa committed Mar 22, 2024
1 parent f227cff commit 8abe70a
Showing 1 changed file with 55 additions and 21 deletions.
76 changes: 55 additions & 21 deletions CHEWBBACA/AlleleCall/allele_call.py
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Original file line number Diff line number Diff line change
Expand Up @@ -663,7 +663,7 @@ def allele_size_classification(sequence_length, locus_mode, size_threshold):


def write_loci_summary(classification_files, output_directory, total_inputs,
classification_labels):
classification_labels, loci_finder):
"""Write a TSV file with classification counts per locus.
Parameters
Expand All @@ -679,6 +679,10 @@ def write_loci_summary(classification_files, output_directory, total_inputs,
classification_labels : list
List with the possible class labels assigned by
chewBBACA.
loci_finder : re.Pattern
Regular expression object to search for loci identifiers
in paths and filenames.
Returns
-------
Expand Down Expand Up @@ -757,7 +761,7 @@ def write_logfile(start_time, end_time, total_inputs,


def write_results_alleles(classification_files, input_identifiers,
output_directory, missing_class):
output_directory, missing_class, loci_finder):
"""Write a TSV file with the allelic profiles for the input samples.
Parameters
Expand All @@ -770,6 +774,9 @@ def write_results_alleles(classification_files, input_identifiers,
Path to the output directory.
missing_class : str
'LNF' if execution mode is 4, 'PLNF' otherwise.
loci_finder : re.Pattern
Regular expression object to search for loci identifiers
in paths and filenames.
Returns
-------
Expand Down Expand Up @@ -823,7 +830,7 @@ def write_results_alleles(classification_files, input_identifiers,

def write_results_statistics(classification_files, input_identifiers,
cds_counts, output_directory, classification_labels,
repeated_counts, invalid_counts):
repeated_counts, invalid_counts, loci_finder):
"""Write a TSV file with classification counts per input.
Parameters
Expand All @@ -849,6 +856,9 @@ def write_results_statistics(classification_files, input_identifiers,
invalid_counts : dict
Dictionary with input identifiers as keys and the total
number of invalid CDSs as values.
loci_finder : re.Pattern
Regular expression object to search for loci identifiers
in paths and filenames.
Returns
-------
Expand Down Expand Up @@ -897,7 +907,7 @@ def write_results_statistics(classification_files, input_identifiers,

def write_results_contigs(classification_files, input_identifiers,
output_directory, cds_coordinates_files,
classification_labels):
classification_labels, loci_finder):
"""Write a TSV file with the CDS coordinates for each input.
Writes a TSV file with coding sequence coordinates (contig
Expand All @@ -921,6 +931,9 @@ def write_results_contigs(classification_files, input_identifiers,
coordinates as values.
classification_labels : list
List with the class labels attributed by chewBBACA.
loci_finder : re.Pattern
Regular expression object to search for loci identifiers
in paths and filenames.
Returns
-------
Expand Down Expand Up @@ -1082,7 +1095,7 @@ def create_unclassified_fasta(fasta_file, prot_file, unclassified_protids,
return output_file


def assign_allele_ids(locus_files, ns, repeated, output_directory):
def assign_allele_ids(locus_files, ns, repeated, output_directory, loci_finder):
"""Assign allele identifiers to CDSs classified as EXC or INF.
Parameters
Expand Down Expand Up @@ -1170,7 +1183,7 @@ def assign_allele_ids(locus_files, ns, repeated, output_directory):


def create_novel_fastas(inferred_alleles, inferred_representatives,
sequences_file, output_directory):
sequences_file, output_directory, loci_finder):
"""Create FASTA files with the novel alleles for each locus.
Parameters
Expand All @@ -1189,6 +1202,9 @@ def create_novel_fastas(inferred_alleles, inferred_representatives,
output_directory : str
Path to the directory where the FASTA files that contain
the novel alleles will be saved to.
loci_finder : re.Pattern
Regular expression object to search for loci identifiers
in paths and filenames.
Returns
-------
Expand Down Expand Up @@ -1238,7 +1254,7 @@ def create_novel_fastas(inferred_alleles, inferred_representatives,
return [total_inferred, total_representatives, updated_novel]


def add_inferred_alleles(inferred_alleles):
def add_inferred_alleles(inferred_alleles, loci_finder):
"""Add inferred alleles to a schema.
Prameters
Expand All @@ -1247,6 +1263,9 @@ def add_inferred_alleles(inferred_alleles):
Dictionary with paths to loci FASTA files in the schema as
keys and paths to the FASTA files that contain the novel
alleles as values.
loci_finder : re.Pattern
Regular expression object to search for loci identifiers
in paths and filenames.
Returns
-------
Expand Down Expand Up @@ -1639,7 +1658,8 @@ def classify_inexact_matches(locus, genomes_matches, inv_map,


def create_missing_fasta(class_files, fasta_file, input_map, dna_hashtable,
output_directory, classification_labels, cds_input):
output_directory, classification_labels, cds_input,
loci_finder):
"""Create Fasta file with sequences for missing data classes.
Parameters
Expand All @@ -1665,6 +1685,9 @@ def create_missing_fasta(class_files, fasta_file, input_map, dna_hashtable,
List with the class labels attributed by chewBBACA.
cds_input : bool
False if there are files with CDS coordinates, True otherwise.
loci_finder : re.Pattern
Regular expression object to search for loci identifiers
in paths and filenames.
Returns
-------
Expand Down Expand Up @@ -1843,7 +1866,7 @@ def count_invalid(input_ids, invalid_seqids, cds_index, distinct_htable):
return invalid_counts


def merge_blast_results(blast_outfiles, output_directory):
def merge_blast_results(blast_outfiles, output_directory, loci_finder):
"""Concatenate BLAST output files based on locus identifier.
Parameters
Expand All @@ -1853,6 +1876,9 @@ def merge_blast_results(blast_outfiles, output_directory):
the locus identifier.
output_directory : str
Path to the output directory.
loci_finder : re.Pattern
Regular expression object to search for loci identifiers
in paths and filenames.
Returns
-------
Expand All @@ -1877,7 +1903,8 @@ def merge_blast_results(blast_outfiles, output_directory):


def allele_calling(fasta_files, schema_directory, temp_directory,
loci_modes, loci_files, config, pre_computed_dir):
loci_modes, loci_files, config, pre_computed_dir,
loci_finder):
"""Perform allele calling for a set of inputs.
Parameters
Expand All @@ -1901,6 +1928,9 @@ def allele_calling(fasta_files, schema_directory, temp_directory,
pre_computed_dir : str
Path to the the directory that contains the files with the
pre-computed hash tables.
loci_finder : re.Pattern
Regular expression object to search for loci identifiers
in paths and filenames.
Returns
-------
Expand Down Expand Up @@ -2361,7 +2391,7 @@ def allele_calling(fasta_files, schema_directory, temp_directory,
# Concatenate files based on locus identifier included in file paths
blast_merged_dir = fo.join_paths(blast_results_dir, ['concatenated'])
fo.create_directory(blast_merged_dir)
concatenated_files = merge_blast_results(blast_files, blast_merged_dir)
concatenated_files = merge_blast_results(blast_files, blast_merged_dir, loci_finder)

# Select best hit per target, filter based on BSR, expand matches
# and get relevant data for classification
Expand Down Expand Up @@ -2762,8 +2792,6 @@ def main(input_file, loci_list, schema_directory, output_directory,
loci_ids = sorted(loci_ids, key=lambda x: len(x), reverse=True)
# Create regex object to search for loci identifiers in paths/strings
loci_finder = re.compile('|'.join(loci_ids))
# Define as global variable to use inside any function
globals()['loci_finder'] = loci_finder

# Create directory to store intermediate files
temp_directory = fo.join_paths(output_directory, ['temp'])
Expand Down Expand Up @@ -2800,7 +2828,8 @@ def main(input_file, loci_list, schema_directory, output_directory,
# Perform allele calling
results = allele_calling(input_files, schema_directory,
temp_directory, loci_modes.copy(),
loci_to_call, config, pre_computed_dir)
loci_to_call, config, pre_computed_dir,
loci_finder)

# Assign allele identifiers, add alleles to schema and create output files
print(f'\n {ct.WRAPPING_UP} ')
Expand All @@ -2823,7 +2852,8 @@ def main(input_file, loci_list, schema_directory, output_directory,
results['int_to_unique'],
output_directory,
results['cds_coordinates'],
classification_labels)
classification_labels,
loci_finder)
outfile, repeated_info, repeated_counts = results_contigs

# Identify paralogous loci
Expand All @@ -2840,7 +2870,7 @@ def main(input_file, loci_list, schema_directory, output_directory,
fo.create_directory(novel_data_directory)
assignment_inputs = list(results['classification_files'].items())
repeated_hashes = set(repeated_info.keys())
assignment_inputs = [[g, ns, repeated_hashes, novel_data_directory, assign_allele_ids]
assignment_inputs = [[g, ns, repeated_hashes, novel_data_directory, loci_finder, assign_allele_ids]
for g in assignment_inputs]

novel_alleles = mo.map_async_parallelizer(assignment_inputs,
Expand Down Expand Up @@ -2911,7 +2941,7 @@ def main(input_file, loci_list, schema_directory, output_directory,
if no_inferred is False:
print('Adding new alleles to schema...')
# Add inferred alleles to schema
alleles_added = add_inferred_alleles(updated_novel)
alleles_added = add_inferred_alleles(updated_novel, loci_finder)
# Recompute mode for loci with novel alleles
print(f'Updating allele size mode values stored in {loci_modes_file}')
for locus_novel in novel_alleles:
Expand All @@ -2929,7 +2959,8 @@ def main(input_file, loci_list, schema_directory, output_directory,
profiles_table = write_results_alleles(list(results['classification_files'].values()),
list(results['int_to_unique'].values()),
output_directory,
classification_labels[-1])
classification_labels[-1],
loci_finder)

# Create file with class counts per input file
print(f'Creating file with class counts per input ({ct.RESULTS_STATISTICS_BASENAME})...')
Expand All @@ -2939,14 +2970,16 @@ def main(input_file, loci_list, schema_directory, output_directory,
output_directory,
classification_labels,
repeated_counts,
results['invalid_alleles'][1])
results['invalid_alleles'][1],
loci_finder)

# Create file with class counts per locus called
print(f'Creating file with class counts per locus ({ct.LOCI_STATS_BASENAME})...')
loci_stats_file = write_loci_summary(results['classification_files'],
output_directory,
len(input_files),
classification_labels)
classification_labels,
loci_finder)

# Create FASTA file with unclassified CDSs
if output_unclassified is True:
Expand All @@ -2968,7 +3001,8 @@ def main(input_file, loci_list, schema_directory, output_directory,
results['dna_hashtable'],
output_directory,
classification_labels,
config['CDS input'])
config['CDS input'],
loci_finder)

# Create FASTA file with inferred alleles
if len(novel_alleles) > 0 and output_novel is True:
Expand Down

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