Mercurial > repos > pcingola > snpeff
comparison snpEff_2_1a/snpEff_2_1a/scripts/data/gmax1.09v8/create.sh @ 3:c052639fa666 default tip
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| author | pcingola |
|---|---|
| date | Fri, 20 Apr 2012 11:22:59 -0400 |
| parents | |
| children |
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| 2:8d0de9212f4f | 3:c052639fa666 |
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| 1 #!/bin/sh -e | |
| 2 | |
| 3 echo "Processing GFF file" | |
| 4 gunzip -c Gmax_109_gene.gff3.gz > genes.gff | |
| 5 # | sed "s/.five_prime_UTR.1//" \ | |
| 6 # | sed "s/.three_prime_UTR.1//" \ | |
| 7 # > genes.gff | |
| 8 | |
| 9 echo "Adding FASTA sequence" | |
| 10 ( echo "###" ; echo "##FASTA" ; gunzip -c Gmax_109.fa.gz ) >> genes.gff | |
| 11 | |
| 12 ehco "Create CDS file" | |
| 13 gunzip -c Gmax_109_cds.fa.gz \ | |
| 14 | sed "s/|PACid:/|PAC:/" \ | |
| 15 | sed "s/Glyma.*|//" \ | |
| 16 > cds.fa | |
| 17 | |
| 18 echo "Create protein file" | |
| 19 gunzip -c Gmax_109_peptide.fa.gz \ | |
| 20 | sed "s/|PACid:/|PAC:/" \ | |
| 21 | sed "s/Glyma.*|//" \ | |
| 22 > protein.fa | |
| 23 | |
| 24 # Build databse | |
| 25 cd $HOME/snpEff | |
| 26 | |
| 27 ./scripts/snpEffM.sh build -v -gff3 gmax1.09v8 2>&1 | tee gmax1.09v8.build | |
| 28 | |
| 29 # CDS test | |
| 30 ./scripts/snpEffM.sh cds -v gmax1.09v8 data/gmax1.09v8/cds.fa 2>&1 | tee gmax1.09v8.cds | |
| 31 | |
| 32 cd - | |
| 33 | |
| 34 echo Done! | |
| 35 |