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Refactor vcf-expression-annotator to be faster #79

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Refactor vcf-expression-annotator to be faster #79

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33 changes: 17 additions & 16 deletions vatools/vcf_expression_annotator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ def to_array(dictionary):

def parse_expression_file(args, vcf_reader, vcf_writer):
if args.format == 'stringtie' and args.mode == 'transcript':
df_all = read_gtf(args.expression_file)
df_all = read_gtf(args.expression_file, usecols=['reference_id', 'transcript_id', 'TPM', 'feature'])
df = df_all[df_all["feature"] == "transcript"]
id_column = resolve_stringtie_id_column(args, df.columns.values)
else:
Expand Down Expand Up @@ -106,24 +106,23 @@ def create_vcf_writer(args, vcf_reader):
output_file = args.output_vcf
return vcfpy.Writer.from_path(output_file, new_header)

def add_expressions(entry, is_multi_sample, sample_name, df, items, tag, id_column, expression_column, ignore_ensembl_id_version, missing_expressions_count, entry_count):
expressions = {}
for item in items:
entry_count += 1
if ignore_ensembl_id_version:
subset = df.loc[df['transcript_without_version'] == re.sub(r'\.[0-9]+$', '', item)]
else:
subset = df.loc[df[id_column] == item]
if len(subset) > 0:
expressions[item] = subset[expression_column].sum()
else:
missing_expressions_count += 1
def add_expressions(entry, is_multi_sample, sample_name, df, items, tag, id_column, expression_column, ignore_ensembl_id_version, missing_expressions_count):
subset = None
if ignore_ensembl_id_version:
items_without_version = [re.sub(r'\.[0-9]+$', '', item) for item in items]
subset = df[df['transcript_without_version'].isin(items_without_version)]
for item in items:
subset.loc[subset['transcript_without_version'] == re.sub(r'\.[0-9]+$', "", item), id_column] = item
else:
subset = df[df[id_column].isin(items)]
expressions = subset[[id_column, expression_column]].groupby(id_column).sum().to_dict()[expression_column]
missing_expressions_count += (len(items) - len(expressions))
if is_multi_sample:
entry.FORMAT += [tag]
entry.call_for_sample[sample_name].data[tag] = to_array(expressions)
else:
entry.add_format(tag, to_array(expressions))
return (entry, missing_expressions_count, entry_count)
return (entry, missing_expressions_count)

def define_parser():
parser = argparse.ArgumentParser(
Expand Down Expand Up @@ -216,11 +215,13 @@ def main(args_input = sys.argv[1:]):
if args.mode == 'gene':
genes = list(genes)
if len(genes) > 0:
(entry, missing_expressions_count, entry_count) = add_expressions(entry, is_multi_sample, args.sample_name, df, genes, 'GX', id_column, expression_column, args.ignore_ensembl_id_version, missing_expressions_count, entry_count)
(entry, missing_expressions_count) = add_expressions(entry, is_multi_sample, args.sample_name, df, genes, 'GX', id_column, expression_column, args.ignore_ensembl_id_version, missing_expressions_count)
entry_count += len(genes)
elif args.mode == 'transcript':
transcript_ids = list(transcript_ids)
if len(transcript_ids) > 0:
(entry, missing_expressions_count, entry_count) = add_expressions(entry, is_multi_sample, args.sample_name, df, transcript_ids, 'TX', id_column, expression_column, args.ignore_ensembl_id_version, missing_expressions_count, entry_count)
(entry, missing_expressions_count) = add_expressions(entry, is_multi_sample, args.sample_name, df, transcript_ids, 'TX', id_column, expression_column, args.ignore_ensembl_id_version, missing_expressions_count)
entry_count += len(transcript_ids)
vcf_writer.write_record(entry)

vcf_reader.close()
Expand Down
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