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Fix mle ValueError on count tables with spaces in sgRNA/gene names (#7) #8

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Merged
davidliwei merged 1 commit into from
Jun 17, 2026
Merged

Fix mle ValueError on count tables with spaces in sgRNA/gene names (#7) #8

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17 changes: 14 additions & 3 deletions mageck2/mleinstanceio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,11 @@ def read_gene_from_file(filename,includesamples=None):
for line in open(filename):
nline+=1
if hascsv==False:
field=line.strip().split()
# split on tab only, consistent with the rest of mageck2 (see mageckCount.py).
# using a generic whitespace split() mis-parses sgRNA/gene names that contain
# spaces (e.g. control entries like "Non-Targeting Control"), shifting the count
# columns and producing a ragged nb_count matrix downstream.
field=line.strip().split('\t')
else:
field=line.strip().split(',')
if nline==1:
Expand Down Expand Up @@ -74,8 +78,15 @@ def read_gene_from_file(filename,includesamples=None):
try:
nrt=float(field[ni+2])+1 # add 1 pseudocount
sks.nb_count[i]+=[nrt]
except ValueError:
print('Error loading line '+str(nline))
except (ValueError,IndexError):
# fail loudly instead of silently skipping the append, which would leave
# nb_count ragged and later crash with an opaque numpy "inhomogeneous shape" error.
logging.error('Failed to parse a numeric read count on line '+str(nline)+
' of '+filename+' (sample column '+str(ni+2)+', value: '+
repr(field[ni+2] if ni+2<len(field) else '<missing>')+
'). Please check that the count table is tab-delimited and that '
'sgRNA/gene names do not contain tabs.')
sys.exit(-1)
# end for loop
logging.info('Loaded '+str(ngene)+' genes.')
#
Expand Down
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