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comparison VCF2Hapmap/vcf2FastaAndHapmap.sh @ 9:98c37a5d67f4 draft

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author dereeper
date Wed, 07 Feb 2018 22:08:47 -0500
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8:6bf69b40365c 9:98c37a5d67f4
1 #!/bin/bash
2
3 tool_path=$(dirname $0)
4
5
6
7 filein=$1
8 fileout_label=$(date "+%Y%m%d%H%M%S")
9 fileout=$2
10 option=$3
11
12 option_text=''
13
14
15 if [ "$option" != "none" ]
16 then fileout_seq=$4
17 fileout_fa1=$5
18 filefasta=$6
19 if [ "$option" == "fasta_gff" ]
20 then filegff=$7
21 fi
22 fi
23
24 if [ "$option" == "fasta" ]
25 then option_text="--reference $filefasta"
26 fi
27
28 if [ "$option" == "fasta_gff" ]
29 then option_text="--reference $filefasta --gff $filegff"
30 fi
31
32
33 perl $tool_path/VCF2FastaAndHapmap.pl --vcf $filein --out $fileout_label $option_text
34
35
36 cp $fileout_label.hapmap $fileout ; rm $fileout_label.hapmap
37
38 if [ "$option" == "fasta_gff" ]
39 then cp $fileout_label.flanking.txt $fileout_seq ; rm $fileout_label.flanking.txt ; cp $fileout_label.gene_alignment.fas $fileout_fa1 ; rm $fileout_label.gene_alignment.fas ;
40 fi
41
42 if [ "$option" == "fasta" ]
43 then cp $fileout_label.flanking.txt $fileout_seq ; rm $fileout_label.flanking.txt ;
44 fi
45