Mercurial > repos > pcingola > snpeff
view snpEff_2_1a/snpEff_2_1a/scripts/data/gmax1.09v8/create.sh @ 3:c052639fa666 default tip
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author | pcingola |
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date | Fri, 20 Apr 2012 11:22:59 -0400 |
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#!/bin/sh -e echo "Processing GFF file" gunzip -c Gmax_109_gene.gff3.gz > genes.gff # | sed "s/.five_prime_UTR.1//" \ # | sed "s/.three_prime_UTR.1//" \ # > genes.gff echo "Adding FASTA sequence" ( echo "###" ; echo "##FASTA" ; gunzip -c Gmax_109.fa.gz ) >> genes.gff ehco "Create CDS file" gunzip -c Gmax_109_cds.fa.gz \ | sed "s/|PACid:/|PAC:/" \ | sed "s/Glyma.*|//" \ > cds.fa echo "Create protein file" gunzip -c Gmax_109_peptide.fa.gz \ | sed "s/|PACid:/|PAC:/" \ | sed "s/Glyma.*|//" \ > protein.fa # Build databse cd $HOME/snpEff ./scripts/snpEffM.sh build -v -gff3 gmax1.09v8 2>&1 | tee gmax1.09v8.build # CDS test ./scripts/snpEffM.sh cds -v gmax1.09v8 data/gmax1.09v8/cds.fa 2>&1 | tee gmax1.09v8.cds cd - echo Done!