Mercurial > repos > dereeper > sniplay3
comparison VCFToolFilter/vcfToolsFilter.sh @ 24:21d878747ac6 draft default tip
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author | dereeper |
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date | Mon, 23 Mar 2015 05:53:20 -0400 |
parents | 8d2d0b6c3521 |
children |
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23:a1ab979f4551 | 24:21d878747ac6 |
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1 #!/bin/bash | |
2 | |
3 tool_path=$(dirname $0) | |
4 | |
5 filein=$1 | |
6 fileout_label=$2 | |
7 fileout=$3 | |
8 filelog=$4 | |
9 export=$5 | |
10 frequency=$6 | |
11 max_freq=$7 | |
12 allow_missing=$8 | |
13 nb_alleles_min=$9 | |
14 nb_alleles_max=${10} | |
15 type=${11} | |
16 bound_start=${12} | |
17 bound_end=${13} | |
18 | |
19 | |
20 if [ "${14}" != "None" ] | |
21 then samples="--samples ${14}" | |
22 fi | |
23 | |
24 if [ "${15}" != "None" ] | |
25 then chromosomes="--chromosomes ${15}" | |
26 fi | |
27 | |
28 if [ "$bound_start" -gt "$bound_end" ] | |
29 then tmp=$bound_start ; bound_start=$bound_end ; bound_end=$tmp ; echo "Warning : Lower bound must be lower than greater bound!" >&2 | |
30 fi | |
31 | |
32 if [ "$nb_alleles_min" -gt "$nb_alleles_max" ] | |
33 then tmp=$nb_alleles_min ; nb_alleles_min=$nb_alleles_max ; nb_alleles_max=$tmp ; echo "Warning : Minimum number of alleles must be lower than maximum number of allele!" >&2 | |
34 fi | |
35 | |
36 perl $tool_path/VCFToolsFilter.pl --input $filein --out $fileout_label --export $export --frequency $frequency --max_freq $max_freq --allow_missing $allow_missing --nb_alleles $nb_alleles_min','$nb_alleles_max --type $type --bounds $bound_start','$bound_end $samples $chromosomes | |
37 | |
38 if [ "$export" = "VCF" ] | |
39 then cp $fileout_label.recode.vcf $fileout ; rm $fileout_label.recode.vcf | |
40 elif [ "$export" = "freq" ] | |
41 then cp $fileout_label.frq $fileout ; rm $fileout_label.frq | |
42 else cp $fileout_label.ped $fileout; cp $fileout_label.map ${16} ; rm $fileout_label.ped $fileout_label.map | |
43 fi | |
44 | |
45 cp vcftools.log $filelog | |
46 rm vcftools.log |