Why you remove file without checking existences?
grep -n os.remove codan.py
106: os.remove(transcripts+".index")
140: os.remove(outF+"minus.fa")
141: os.remove(outF+"minus.fa.index")
287: os.remove(outF+"ORFs_plus.gtf")
288: os.remove(outF+"ORFs_minus.gtf")
289: os.remove(outF+"minus.fa")
290: os.remove(outF+"minus.fa.index")
291: os.remove(transcripts+".index")
All of these may cause error like following when the output directory is empty(or run codan first time).
Traceback (most recent call last):
File "/Bio/User/kxie/pipeline/geneAnnot/bin/codan/bin/codan.py", line 524, in main()
File "/Bio/User/kxie/pipeline/geneAnnot/bin/codan/bin/codan.py", line 506, in main
_codanBOTH(options.transcripts, options.output_folder, options.model, options.cpu)
File "/Bio/User/kxie/pipeline/geneAnnot/bin/codan/bin/codan.py", line 355, in _codanBOTH
_retrieveORFBOTH(transcripts, outF+"minus.fa", outF)
File "/Bio/User/kxie/pipeline/geneAnnot/bin/codan/bin/codan.py", line 290, in _retrieveORFBOTH
os.remove(outF+"minus.fa.index")
FileNotFoundError: [Errno 2] No such file or directory: './02.ccs/codan/minus.fa.index'
Would you please disable the removings or check existences first?
xiekunwhy
commented
2 years ago
Hi,
Why you remove file without checking existences? grep -n os.remove codan.py 106: os.remove(transcripts+".index") 140: os.remove(outF+"minus.fa") 141: os.remove(outF+"minus.fa.index") 287: os.remove(outF+"ORFs_plus.gtf") 288: os.remove(outF+"ORFs_minus.gtf") 289: os.remove(outF+"minus.fa") 290: os.remove(outF+"minus.fa.index") 291: os.remove(transcripts+".index") All of these may cause error like following when the output directory is empty(or run codan first time). Traceback (most recent call last): File "/Bio/User/kxie/pipeline/geneAnnot/bin/codan/bin/codan.py", line 524, in
main()
File "/Bio/User/kxie/pipeline/geneAnnot/bin/codan/bin/codan.py", line 506, in main
_codanBOTH(options.transcripts, options.output_folder, options.model, options.cpu)
File "/Bio/User/kxie/pipeline/geneAnnot/bin/codan/bin/codan.py", line 355, in _codanBOTH
_retrieveORFBOTH(transcripts, outF+"minus.fa", outF)
File "/Bio/User/kxie/pipeline/geneAnnot/bin/codan/bin/codan.py", line 290, in _retrieveORFBOTH
os.remove(outF+"minus.fa.index")
FileNotFoundError: [Errno 2] No such file or directory: './02.ccs/codan/minus.fa.index'
Would you please disable the removings or check existences first?
Best, Kun