Mercurial > repos > dereeper > plink
comparison plink.sh @ 0:fe39a4677281 draft
Uploaded
| author | dereeper |
|---|---|
| date | Fri, 05 Aug 2016 09:46:55 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:fe39a4677281 |
|---|---|
| 1 #!/bin/bash | |
| 2 | |
| 3 | |
| 4 tool_path=$(dirname $0) | |
| 5 | |
| 6 filein=$1 | |
| 7 fileout_label=$(date "+%Y%m%d%H%M%S") | |
| 8 fileout=$2 | |
| 9 filelog=$3 | |
| 10 frequency=$4 | |
| 11 max_freq=$5 | |
| 12 allow_missing=$6 | |
| 13 type=${7} | |
| 14 bound_start=${8} | |
| 15 bound_end=${9} | |
| 16 | |
| 17 cp -rf $filein input$$.vcf | |
| 18 | |
| 19 if [ "${10}" != "None" ] | |
| 20 then samples="--samples ${10}" | |
| 21 fi | |
| 22 | |
| 23 if [ "${11}" != "None" ] | |
| 24 then chromosomes="--chromosomes ${11}" | |
| 25 fi | |
| 26 | |
| 27 if [ "$bound_start" -gt "$bound_end" ] | |
| 28 then tmp=$bound_start ; bound_start=$bound_end ; bound_end=$tmp ; echo "Warning : Lower bound must be lower than greater bound!" >&2 | |
| 29 fi | |
| 30 | |
| 31 | |
| 32 export="VCF" | |
| 33 | |
| 34 perl $tool_path/Plink.pl --input input$$.vcf --out $fileout_label --export $export --frequency $frequency --max_freq $max_freq --allow_missing $allow_missing --type $type --bounds $bound_start','$bound_end $samples $chromosomes | |
| 35 | |
| 36 | |
| 37 #echo ${16} >>$fileout_label.log | |
| 38 #echo ${15} >>$fileout_label.log | |
| 39 #echo ${17} >>$fileout_label.log | |
| 40 #echo ${18} >>$fileout_label.log | |
| 41 | |
| 42 if [ "$export" = "VCF" ] | |
| 43 then cp $fileout_label.vcf $fileout ; rm $fileout_label.vcf | |
| 44 else cp $fileout_label.bed $fileout; cp $fileout_label.bed ${15} ; cp $fileout_label.bim ${18} ;rm $fileout_label.bed $fileout_label.fam $fileout_label.bim | |
| 45 fi | |
| 46 | |
| 47 cp $fileout_label.log $filelog | |
| 48 rm $fileout_label.log | |
| 49 |