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I use it to identify junctions in reads, but if there is no junction in reads the JWR_checker.py raise an error due to pandas.concat() function at line 294. Then, as I integrated NanoSplicer in Nextflow, my workflow stops. So I can suggest this to replace JWR_checker.py line 294 to 301:
d_list = [x.result() for x in futures if x.result() is not None]
if d_list:
d = pd.concat(d_list)
d.to_hdf(param.outfile, 'data')
pd.DataFrame([]).to_hdf(param.outfile, 'skipped')
# output csv file if required
if param.output_csv:
d.to_csv(param.outfile + ".csv")
else:
empty_data = pd.DataFrame({
'id': [],
'mapQ': [],
'transcript_strand': [],
'chrID': [],
'loc': [],
'JAQ': []
})
empty_data.to_hdf(param.outfile, 'data')
pd.DataFrame([]).to_hdf(param.outfile, 'skipped')
if param.output_csv:
empty_data.to_csv(param.outfile + ".csv")
The aim is to return an empty h5 and/or csv as result.
I didn't test the following steps such as JWR_subset.py or NanoSplicer.py.
Cheers !
The text was updated successfully, but these errors were encountered:
Thanks for this great tool !
I use it to identify junctions in reads, but if there is no junction in reads the JWR_checker.py raise an error due to pandas.concat() function at line 294. Then, as I integrated NanoSplicer in Nextflow, my workflow stops. So I can suggest this to replace JWR_checker.py line 294 to 301:
The aim is to return an empty h5 and/or csv as result.
I didn't test the following steps such as JWR_subset.py or NanoSplicer.py.
Cheers !
The text was updated successfully, but these errors were encountered: