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Debug predict #5

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Debug predict #5

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cc96f0f
Fixing typos in scalop predict, adding kwargs argument to assign so t…
exs-dcutting May 5, 2023
23afec7
Merge branch 'oxpig:master' into debug_predict
exs-dcutting Sep 18, 2023
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8 changes: 4 additions & 4 deletions build/lib/scalop/predict.py
100644 → 100755
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Original file line number Diff line number Diff line change
Expand Up @@ -201,7 +201,7 @@ def assigncmd(args):
print('Write results to %s' % opf)
return assignresults

def assign(seq,scheme='imgt',definition='north',dbv='latest',structuref='',loopdb='',hc='',lc='',blacklist=[]):
def assign(seq,scheme='imgt',definition='north',dbv='latest',structuref='',loopdb='',hc='',lc='',blacklist=[], **kwargs):
'''
args: <sequence(s)> <numbering scheme> <cdr definition> <db version> <structure file> <loop database directory> <heavy chain ID> <light chain ID> <blacklisted PDB_CHAIN IDs>
'''
Expand All @@ -217,8 +217,8 @@ def assign(seq,scheme='imgt',definition='north',dbv='latest',structuref='',loopd
seqh,seql = seq.split('/')
seqh = re.sub('[\W]+','',seqh)
seql = re.sub('[\W]+','',seql)
seqs.append(('{}_1'.format(seqi),seqh))
seqs.append(('{}_2'.format(seqi),seql))
seqs.append(('{}_1'.format(seqid),seqh))
seqs.append(('{}_2'.format(seqid),seql))
else:
seqs.append((seqid,re.sub('[\W\/]+','',seq)))
elif type(seq) == dict: # in dict
Expand Down Expand Up @@ -251,7 +251,7 @@ def assign(seq,scheme='imgt',definition='north',dbv='latest',structuref='',loopd

ncpu = multiprocessing.cpu_count()

numberedseqs = run_anarci( seqs,scheme=scheme,ncpu=ncpu,assign_germline=False)
numberedseqs = run_anarci(seqs,scheme=scheme,ncpu=ncpu,assign_germline=False, **kwargs)

# Import the right version of pssm database
ip(scheme,definition,dbv)
Expand Down
8 changes: 4 additions & 4 deletions lib/python/scalop/predict.py
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Original file line number Diff line number Diff line change
Expand Up @@ -201,7 +201,7 @@ def assigncmd(args):
print('Write results to %s' % opf)
return assignresults

def assign(seq,scheme='imgt',definition='north',dbv='latest',structuref='',loopdb='',hc='',lc='',blacklist=[]):
def assign(seq,scheme='imgt',definition='north',dbv='latest',structuref='',loopdb='',hc='',lc='',blacklist=[], **kwargs):
'''
args: <sequence(s)> <numbering scheme> <cdr definition> <db version> <structure file> <loop database directory> <heavy chain ID> <light chain ID> <blacklisted PDB_CHAIN IDs>
'''
Expand All @@ -217,8 +217,8 @@ def assign(seq,scheme='imgt',definition='north',dbv='latest',structuref='',loopd
seqh,seql = seq.split('/')
seqh = re.sub('[\W]+','',seqh)
seql = re.sub('[\W]+','',seql)
seqs.append(('{}_1'.format(seqi),seqh))
seqs.append(('{}_2'.format(seqi),seql))
seqs.append(('{}_1'.format(seqid),seqh))
seqs.append(('{}_2'.format(seqid),seql))
else:
seqs.append((seqid,re.sub('[\W\/]+','',seq)))
elif type(seq) == dict: # in dict
Expand Down Expand Up @@ -251,7 +251,7 @@ def assign(seq,scheme='imgt',definition='north',dbv='latest',structuref='',loopd

ncpu = multiprocessing.cpu_count()

numberedseqs = run_anarci( seqs,scheme=scheme,ncpu=ncpu,assign_germline=False)
numberedseqs = run_anarci(seqs,scheme=scheme,ncpu=ncpu,assign_germline=False, **kwargs)

# Import the right version of pssm database
ip(scheme,definition,dbv)
Expand Down