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dsturg / Spanki

Splicing analysis toolkit for RNA-SEQ
http://www.cbcb.umd.edu/software/spanki/
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keyerror "chr9" #10

Open liushang17 opened 2 years ago

liushang17 commented 2 years ago

Hi, I meet this problem in spankisim_transcripts, and I could not solve it. [Jan 26 10:06:13] Done loading annotation as bam Simulating 400 transcripts

Traceback (most recent call last): File "/jdfssz1/ST_SUPERCELLS/P21Z10200N0134/USER/liushang/Spanki-master/bin/spankisim_transcripts", line 1580, in sys.exit(main()) File "/jdfssz1/ST_SUPERCELLS/P21Z10200N0134/USER/liushang/Spanki-master/bin/spankisim_transcripts", line 1294, in main myseq_spliced, myseq_unspliced = getTxSequence(TX[mytx],f) File "/jdfssz1/ST_SUPERCELLS/P21Z10200N0134/USER/liushang/Spanki-master/bin/spankisim_transcripts", line 87, in getTxSequence txseq_unspliced += Seq(f[chr][mypos_unspliced:mypos_unspliced + chunklength], IUPAC.unambiguous_dna) File "/jdfssz1/ST_SUPERCELLS/P21Z10200N0134/USER/liushang/software/miniconda3/envs/py2/lib/python2.7/site-packages/pyfasta/fasta.py", line 128, in getitem c = self.index[i] KeyError: 'chr9'

It seems the problem resulting from 'f'. Thanks!!!