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Merged
DarioMarzella merged 1 commit into from
May 1, 2025
Merged

Issue_297 #300

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7 changes: 4 additions & 3 deletions PANDORA/Pandora/Modelling_functions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -147,7 +147,7 @@ def predict_anchors_netMHCIIpan(peptide, allele_type, output_dir, verbose=True,
all_netMHCpan_alleles.append(line.split()[0].replace('\n', ''))

# Format the alles to netMHCIIpan readable format
target_alleles = [i.split('-')[-1].replace('*', '_') for i in allele_type]
target_alleles = [i.split('-')[-1].replace('*', '_').replace(':','') for i in allele_type]

# The DQ and DP alleles only function in pairs in netMHCIIpan, which we cannot match from our alleles
# So take the first 3 partially matched allele combinations
Expand All @@ -174,9 +174,10 @@ def predict_anchors_netMHCIIpan(peptide, allele_type, output_dir, verbose=True,
if target_alleles == [] and any(al.startswith('H2') for al in allele_type):
target_alleles = [i for i in all_netMHCpan_alleles if i.startswith('H-')]

# If there is no target allele that occurs in netMHCIIpan, just use the standard DRB1_0101
# If there is no target allele that occurs in netMHCIIpan, raise an Exception
if target_alleles == []:
target_alleles = ['DRB1_0101']
#target_alleles = ['DRB1_0101']
raise Exception('ERROR: Provided allele is not available in netMHCIIpan-4.1.\n')

target_alleles_str = ','.join(target_alleles)

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