Commit e67232a2 authored by Romain Feron's avatar Romain Feron
Browse files

fixed bugs in loading data from catalog

parent 562d4880
......@@ -88,19 +88,16 @@ def get_haplotypes(parameters, sequence=False, correspondance=False, numbers=Tru
locus_id = tabs[2]
indiv_ids = tabs[8].split(',')
haplotypes_data[locus_id] = {'n_males': 0, 'n_females': 0}
for individual in indiv_ids:
temp = individual.split('_')[0]
if correspondance:
haplotypes_data[locus_id]['individuals'][individual.split('_')[0]] = individual.split('_')[1]
else:
haplotypes_data[locus_id]['individuals'] = [individual.split('_')[0] for individual in indiv_ids]
if numbers:
if parameters.popmap[parameters.order[temp[0]]] is 'M':
haplotypes_data[locus_id]['n_males'] += 1
elif parameters.popmap[parameters.order[temp[0]]] is 'F':
haplotypes_data[locus_id]['n_females'] += 1
if sequence:
haplotypes_data[locus_id]['sequence'] = tabs[9]
temp = [[individual.split('_')[0], individual.split('_')[1]] for individual in indiv_ids]
if correspondance:
haplotypes_data[locus_id]['individuals'] = {t[0]: t[1] for t in temp}
else:
haplotypes_data[locus_id]['individuals'] = [t[0] for t in temp]
if numbers:
haplotypes_data[locus_id]['n_males'] = [parameters.popmap[parameters.order[i[0]]] for i in temp].count('M')
haplotypes_data[locus_id]['n_females'] = [parameters.popmap[parameters.order[i[0]]] for i in temp].count('F')
if sequence:
haplotypes_data[locus_id]['sequence'] = tabs[9]
catalog.close()
......
......@@ -5,7 +5,7 @@ from radseq_analysis import output
def analysis(parameters):
print(' - Loading haplotypes file ...')
haplotypes = file_handler.get_haplotypes(parameters)
haplotypes = file_handler.get_haplotypes(parameters, sequence=True)
print(' - Filtering loci ...')
output.sex_linked_haplotypes(parameters, haplotypes)
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