Please see my error trying to preprocess using kma
lynnyi⟫ python2.7 /home/lynnyi/R/x86_64-pc-linux-gnu-library/3.4/kma/pre-process/generate_introns.py --genome ~/genomes/Mus_musculus.GRCm38.dna.alt.fa --gtf ~/genomes/Mus_musculus.GRCm38.91.gtf --extend 20 --out ~/introns INFO: Reading in GTF: /home/lynnyi/genomes/Mus_musculus.GRCm38.91.gtf
INFO: Grouping transcripts by gene
INFO: Writing intron BED file: /home/lynnyi/introns/introns.bed
INFO: Computing intron-to-transcript compatability
INFO: Opening FASTA: /home/lynnyi/genomes/Mus_musculus.GRCm38.dna.alt.fa
INFO: Note: will take a while the first time it is opened.
Traceback (most recent call last):
File "/home/lynnyi/R/x86_64-pc-linux-gnu-library/3.4/kma/pre-process/generate_introns.py", line 154, in
main()
File "/home/lynnyi/R/x86_64-pc-linux-gnu-library/3.4/kma/pre-process/generate_introns.py", line 151, in main
bed_to_introns(bed_out, args.genome, introns_out)
File "/home/lynnyi/R/x86_64-pc-linux-gnu-library/3.4/kma/pre-process/generate_introns.py", line 55, in bed_to_introns
seq = fasta[ref][int(start):int(stop)]
File "/usr/local/lib/python2.7/dist-packages/pyfasta/fasta.py", line 128, in getitem
c = self.index[i]
KeyError: '3'
Please see my error trying to preprocess using kma
lynnyi⟫ python2.7 /home/lynnyi/R/x86_64-pc-linux-gnu-library/3.4/kma/pre-process/generate_introns.py --genome ~/genomes/Mus_musculus.GRCm38.dna.alt.fa --gtf ~/genomes/Mus_musculus.GRCm38.91.gtf --extend 20 --out ~/introns INFO: Reading in GTF: /home/lynnyi/genomes/Mus_musculus.GRCm38.91.gtf INFO: Grouping transcripts by gene INFO: Writing intron BED file: /home/lynnyi/introns/introns.bed INFO: Computing intron-to-transcript compatability INFO: Opening FASTA: /home/lynnyi/genomes/Mus_musculus.GRCm38.dna.alt.fa INFO: Note: will take a while the first time it is opened. Traceback (most recent call last): File "/home/lynnyi/R/x86_64-pc-linux-gnu-library/3.4/kma/pre-process/generate_introns.py", line 154, in
main()
File "/home/lynnyi/R/x86_64-pc-linux-gnu-library/3.4/kma/pre-process/generate_introns.py", line 151, in main
bed_to_introns(bed_out, args.genome, introns_out)
File "/home/lynnyi/R/x86_64-pc-linux-gnu-library/3.4/kma/pre-process/generate_introns.py", line 55, in bed_to_introns
seq = fasta[ref][int(start):int(stop)]
File "/usr/local/lib/python2.7/dist-packages/pyfasta/fasta.py", line 128, in getitem
c = self.index[i]
KeyError: '3'