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Remove sample name parsing which doesn't work when directories have .… #100

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Remove sample name parsing which doesn't work when directories have .…
ericenns Nov 28, 2017
c5bff33
Added in missing )
ericenns Dec 14, 2017
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14 changes: 7 additions & 7 deletions scripts/srst2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -311,7 +311,7 @@ def parse_fai(fai_file,db_type,delimiter):
return size, gene_clusters, unique_gene_symbols, unique_allele_symbols, gene_cluster_symbols


def read_pileup_data(pileup_file, size, prob_err, consensus_file = ""):
def read_pileup_data(pileup_file, size, prob_err, sample_name, consensus_file = ""):
with open(pileup_file) as pileup:
prob_success = 1 - prob_err # Set by user, default is prob_err = 0.01
hash_alignment = {}
Expand Down Expand Up @@ -450,7 +450,7 @@ def read_pileup_data(pileup_file, size, prob_err, consensus_file = ""):
elif consensus_file.split(".")[-2] == "all_consensus_alleles":
consensus_type = "consensus"
with open(consensus_file, "a") as consensus_outfile:
consensus_outfile.write(">{0}.{1} {2}\n".format(allele, consensus_type, pileup_file.split(".")[1].split("__")[1]))
consensus_outfile.write(">{0}.{1} {2}\n".format(allele, consensus_type, sample_name)

@mbargull mbargull Dec 14, 2017

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typo: missing )

outstring = consensus_seq + "\n"
consensus_outfile.write(outstring)

Expand Down Expand Up @@ -942,7 +942,7 @@ def dict_of_dicts_inverted_ind(dd):
def parse_scores(run_type,args,scores, hash_edge_depth,
avg_depth_allele, coverage_allele, mismatch_allele, indel_allele,
missing_allele, size_allele, next_to_del_depth_allele,
unique_cluster_symbols,unique_allele_symbols, pileup_file):
unique_cluster_symbols,unique_allele_symbols, pileup_file, sample_name):

# sort into hash for each gene locus
scores_by_gene = group_allele_dict_by_gene(dict( (allele,val) for (allele,val) in scores.items() \
Expand Down Expand Up @@ -1018,11 +1018,11 @@ def parse_scores(run_type,args,scores, hash_edge_depth,
if args.report_new_consensus or args.report_all_consensus:
new_alleles_filename = args.output + ".new_consensus_alleles.fasta"
allele_pileup_file = create_allele_pileup(results[gene][0], pileup_file)
read_pileup_data(allele_pileup_file, size_allele, args.prob_err, consensus_file = new_alleles_filename)
read_pileup_data(allele_pileup_file, size_allele, args.prob_err, sample_name, consensus_file = new_alleles_filename)
if args.report_all_consensus:
new_alleles_filename = args.output + ".all_consensus_alleles.fasta"
allele_pileup_file = create_allele_pileup(results[gene][0], pileup_file)
read_pileup_data(allele_pileup_file, size_allele, args.prob_err, consensus_file = new_alleles_filename)
read_pileup_data(allele_pileup_file, size_allele, args.prob_err, sample_name, consensus_file = new_alleles_filename)

return results # (allele, diffs, depth_problem, divergence)

Expand Down Expand Up @@ -1419,7 +1419,7 @@ def map_fileSet_to_db(args, sample_name, fastq_inputs, db_name, fasta, size, gen
logging.info(' Processing SAMtools pileup...')
hash_alignment, hash_max_depth, hash_edge_depth, avg_depth_allele, coverage_allele, \
mismatch_allele, indel_allele, missing_allele, size_allele, next_to_del_depth_allele= \
read_pileup_data(pileup_file, size, args.prob_err)
read_pileup_data(pileup_file, size, args.prob_err, sample_name)

# Generate scores for all alleles (prints these and associated info if verbose)
# result = dict, with key=allele, value=score
Expand All @@ -1437,7 +1437,7 @@ def map_fileSet_to_db(args, sample_name, fastq_inputs, db_name, fasta, size, gen
allele_scores = parse_scores(run_type, args, scores, \
hash_edge_depth, avg_depth_allele, coverage_allele, mismatch_allele, \
indel_allele, missing_allele, size_allele, next_to_del_depth_allele,
unique_gene_symbols, unique_allele_symbols, pileup_file)
unique_gene_symbols, unique_allele_symbols, pileup_file, sample_name)

# REPORT/RECORD RESULTS

Expand Down