Where could I find extract_fasta?

LorenaDerezanin commented 6 years ago

Hello Lex, I'm adjusting your Gene_mining.slurm script from S19_genome_mining_and_gene_identification/scripts to mine mammal immune genes but I got stuck at the extract_fasta step. I assume this command merges all the unitig reads(containing predicted ORFs) with the same prefix in the file name, but I was wondering how it merges unitig IDs. Is extract_fasta a part of some particular package or you maybe have it stuck somewhere? I would appreciate a lot if you could share that piece of code.

Thank you! Lorena

lexnederbragt commented 6 years ago

I hope @mmatschiner can answer this one...

mmatschiner commented 6 years ago

No, but @martinmalmstrom might?

LorenaDerezanin commented 6 years ago

Hi again gents,

it seems it's been awhile since you've been working on this script :D so I wanted to suggest a somewhat easier solution if you don't mind, and that is to please send me an example of the output file in the following step if possible:

    for f in ORFs/*; do \
        extract_fasta $f \
        >> ${f%_splitted_utg_reads_???}"_merged_ORFs" \
        ; done
    cd ORFs
    mkdir ORFs_FASTA
    mv *_ORFs ORFs_FASTA
    echo "6) Utg-ORFs predicted and parsed" \
       >> ~/Progressreports_2015/Progress_$FISH

so I could perhaps reconstruct the extract_fasta command and write it on my own based on one of the output files with the "_merged_ORFs" suffix.

Thank you for your effort! Lorena

uio-cees / teleost_genomes_immune

Where could I find extract_fasta? #1