I am trying to use mafToFastaStitcher with a maf and set of fastas that I have generated using biopython (attached). However, I get the following error:
Error, unanticipated character in DNA sequence:
From looking at the underlying code (sharedMaf.c), I suspect that this is because my maf file is not being parsed properly, possibly due to an issue with the format. Can anyone tell what this issue is and how I may resolve it?
Here is how I called mafToFastaStitcher:
mafToFastaStitcher --maf subsetMaf_1041430-1041520.maf --seqs cat list_of_fas1041430-1041520.txt --outMfa testStitcher.mfa --breakpointPenalty 1 --interstitialSequence 20
I am trying to use mafToFastaStitcher with a maf and set of fastas that I have generated using biopython (attached). However, I get the following error: Error, unanticipated character in DNA sequence: From looking at the underlying code (sharedMaf.c), I suspect that this is because my maf file is not being parsed properly, possibly due to an issue with the format. Can anyone tell what this issue is and how I may resolve it?
Here is how I called mafToFastaStitcher: mafToFastaStitcher --maf subsetMaf_1041430-1041520.maf --seqs
cat list_of_fas1041430-1041520.txt--outMfa testStitcher.mfa --breakpointPenalty 1 --interstitialSequence 20Thank you!
list_of_fas1041430-1041520.txt subset_aln1041430-1041476.fa.txt subset_aln1041477-1041481.fa.txt subset_aln1041482-1041514.fa.txt subset_aln1041515-1041539.fa.txt subsetMaf_1041430-1041520.maf.txt