Mercurial > repos > pcingola > snpeff
comparison snpEff_2_1a/snpEff_2_1a/scripts/data/SL2.40/create.sh @ 3:c052639fa666 default tip
Uploaded
| author | pcingola |
|---|---|
| date | Fri, 20 Apr 2012 11:22:59 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 2:8d0de9212f4f | 3:c052639fa666 |
|---|---|
| 1 #!/bin/sh | |
| 2 | |
| 3 # wget ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/wgs/assembly/build_2.40/S_lycopersicum_chromosomes.2.40.fa.gz | |
| 4 | |
| 5 # GFF has to be downloaded manually from | |
| 6 # | |
| 7 # http://solgenomics.net/itag/release/2.3/list_files# | |
| 8 # File ITAG2.3_gene_models.gff3 | |
| 9 # | |
| 10 # | |
| 11 | |
| 12 # Create genes.gff | |
| 13 echo Decompressing the file | |
| 14 cp ITAG2.3_gene_models.gff3.gz genes.gff.gz | |
| 15 rm -f genes.gff | |
| 16 gunzip genes.gff.gz | |
| 17 | |
| 18 echo Fixing start-end problem | |
| 19 cat genes.gff | ./fixStartEnd.pl > g | |
| 20 mv g genes.gff | |
| 21 | |
| 22 # Append FASTA Sequences | |
| 23 echo "###" >> genes.gff | |
| 24 echo "##FASTA" >> genes.gff | |
| 25 zcat S_lycopersicum_chromosomes.2.40.fa.gz >> genes.gff | |
| 26 |