search

berman-lab / ymap

YMAP - Yeast Mapping Analysis Pipeline : An online pipeline for the analysis of yeast genomic datasets.
MIT License
6 stars 6 forks source link

FASTA index creation error #60

Closed darrenabbey closed 7 years ago

darrenabbey commented 7 years ago

When input genome FASTA file is initially processed by "[Ymap_root]/scripts_seqModules/FASTA_reformat_1.sh" and "[Ymap_root]/scripts_seqModules/FASTA_reformat_1.sh", blank lines are introduced between FASTA entries. These lines result in error while regenerating FASTA index file using SamTools (ver. samtools-0.1.3_x86_64-linux) later in script "[Ymap_root]/scripts_genomes/genome.install_6.sh".

Error text includes: "different line length in sequence"

darrenabbey commented 7 years ago

The fix I'm using updates "[Ymap_root]/scripts_seqModules/FASTA_reformat_2.sh" with:

    # 3) Remove blank lines, which were added as artifact of putting newlines between entries.
    sed '/^\s*$/d' $1 >> $1.temp
    rm $1;
    mv $1.temp $1;

I'm still catching up with GIT management and didn't want to dump it to the repo in the wrong way.

darrenabbey commented 7 years ago

And then I realized I had an old version of samtools installed, even after I actively went to download the right one. closing.