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 |
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date | Fri, 20 Apr 2012 11:22:59 -0400 |
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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 |