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RTRichar / MetaCurator

GNU General Public License v3.0
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input.fasta needs to be single-line? #5

Closed hughcross closed 3 years ago

hughcross commented 4 years ago

Hello,

I ran the IterRazor.py script on a dataset and got zero results. I noticed that the test file was single line, whereas mine were multi-line (e.g. wrapped at 80 bp). I converted the input sequences to single line fasta, and then it worked. I did not see this mentioned anywhere in the documentation, but I am sorry if I missed it.

Just in case someone needs it, the awk one-liner I used to convert the fasta file is below (there are lots of solutions out there, but I always end up hunting for it):

awk '{if(NR==1) {print $0} else {if($0 ~ /^>/) {print "\n"$0} else {printf $0}}}' input_multiline.fasta > output_oneline.fasta
RTRichar commented 3 years ago

Hi Hugh, I apologize for the very long delay in my response here. Thanks for pointing out these issues though. I went ahead and added a comment to the Readme about the the fasta formatting and updated the manual.

Best, Rodney