I met some problems (not the latest docker image). After checking my gff3 file and getRightStrand.py I found that error occurred when a gene contained an mRNA but lost CDS, just the situation in my gffs file. It seems to be different from the closed issue, though the error message is similar. I am worried that the latest image and the modification were not fit to the situation i encountered.
After modifying the code
if(len(position)<1):
continue
the errors seem to disappear.
Traceback (most recent call last):
File "/opt/LoReAn/code/lorean.py", line 610, in
main()
File "/opt/LoReAn/code/lorean.py", line 568, in main
update3_1 = grs.remove_redudant(ref_rename, update2)
File "/opt/LoReAn/code/getRightStrand.py", line 873, in remove_redudant
fasta = pep_seq(genome, final_evm)
File "/opt/LoReAn/code/getRightStrand.py", line 774, in pep_seq
t.start = position[0]
IndexError: list index out of range
I met some problems (not the latest docker image). After checking my gff3 file and getRightStrand.py I found that error occurred when a gene contained an mRNA but lost CDS, just the situation in my gffs file. It seems to be different from the closed issue, though the error message is similar. I am worried that the latest image and the modification were not fit to the situation i encountered.
After modifying the code
if(len(position)<1):
continue
the errors seem to disappear.
Traceback (most recent call last):
File "/opt/LoReAn/code/lorean.py", line 610, in
main()
File "/opt/LoReAn/code/lorean.py", line 568, in main
update3_1 = grs.remove_redudant(ref_rename, update2)
File "/opt/LoReAn/code/getRightStrand.py", line 873, in remove_redudant
fasta = pep_seq(genome, final_evm)
File "/opt/LoReAn/code/getRightStrand.py", line 774, in pep_seq
t.start = position[0]
IndexError: list index out of range