Mercurial > repos > davidvanzessen > baseline_bayesian_estimation

comparison wrapper.sh @ 6:8a4183eed741 draft

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author davidvanzessen
date Mon, 18 Aug 2014 05:28:47 -0400
parents d8de51314d3f
children 45a5e3bd9df4
comparison
equal deleted inserted replaced
5:d8de51314d3f 6:8a4183eed741
45 echo "id=$id" 45 echo "id=$id"
46 unzip $current -d $PWD/$id/ >> $PWD/unziplog.log 46 unzip $current -d $PWD/$id/ >> $PWD/unziplog.log
47 summaryfile="$PWD/summary_${id}.txt" 47 summaryfile="$PWD/summary_${id}.txt"
48 gappedfile="$PWD/gappednt_${id}.txt" 48 gappedfile="$PWD/gappednt_${id}.txt"
49 filtered="$PWD/filtered_${id}.txt" 49 filtered="$PWD/filtered_${id}.txt"
50 cat $PWD/$id/*/1_* > $summaryfile 50 filecount=`ls -l $PWD/$id/ | wc -l`
51 cat $PWD/$id/*/2_* > $gappedfile 51 if [ "$filecount" -eq "1" ]
52 then
53 cat $PWD/$id/*/1_* > $summaryfile
54 cat $PWD/$id/*/2_* > $gappedfile
55 else
56 cat $PWD/$id/1_* > $summaryfile
57 cat $PWD/$id/2_* > $gappedfile
58 fi
52 Rscript $dir/filter.r $summaryfile $gappedfile "$selection" $filtered 2>&1 59 Rscript $dir/filter.r $summaryfile $gappedfile "$selection" $filtered 2>&1
53 60
54 final="$PWD/final_${id}.txt" 61 final="$PWD/final_${id}.txt"
55 cat $filtered | cut -f2,4,7 > $final 62 cat $filtered | cut -f2,4,7 > $final
56 python $dir/script_imgt.py --input $final --ref $ref --output $fasta --id $id 63 python $dir/script_imgt.py --input $final --ref $ref --output $fasta --id $id