50 lines
1.5 KiB
Bash
Executable File
50 lines
1.5 KiB
Bash
Executable File
#!/bin/bash
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is_ctg=0
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if [ $# -gt 1 ] && [ $1 == '-A' ]; then
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is_ctg=1
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shift
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fi
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if [ $# -lt 2 ]; then
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echo "Usage: $0 [-A] <prefix> <gene>"
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exit 1
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fi
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preres="resource-human-HLA"
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root=`dirname $0`
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pre=$1.$2
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touch $pre.gt
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if [ ! -s $pre.fq ]; then
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echo '** Empty input file. Abort!' >&2
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exit 0
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fi
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if [ $is_ctg -eq 0 ]; then
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echo "** De novo assembling..." >&2
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len=`$root/seqtk comp $pre.fq | awk '{++x;y+=$2}END{printf("%.0f\n", y/x)}'`
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$root/fermi2.pl unitig -f $root/fermi2 -r $root/ropebwt2 -t2 -l$len -p $pre.tmp $pre.fq > $pre.tmp.mak
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make -f $pre.tmp.mak >&2
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cp $pre.tmp.mag.gz $pre.mag.gz
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else
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rm -f $pre.tmp.mag.gz
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ln -s $pre.fq $pre.tmp.mag.gz
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fi
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echo "** Selecting contigs overlapping target exons..." >&2
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(ls $root/$preres/HLA-ALT-idx/*.fa.bwt | sed s,.bwt,, | xargs -i $root/bwa mem -t2 -B1 -O1 -E1 {} $pre.tmp.mag.gz 2>/dev/null) | grep -v ^@ | sort -k3,3 -k4,4n | gzip > $pre.tmp.ALT.sam.gz
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$root/k8 $root/typeHLA-selctg.js $2 $root/$preres/HLA-ALT-exons.bed $pre.tmp.ALT.sam.gz | $root/seqtk subseq $pre.tmp.mag.gz - | gzip -1 > $pre.tmp.fq.gz
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echo "** Mapping exons to de novo contigs..." >&2
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$root/bwa index -p $pre.tmp $pre.tmp.fq.gz 2>/dev/null
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$root/seqtk comp $root/$preres/HLA-CDS.fa | cut -f1 | grep ^$2 | $root/seqtk subseq $root/$preres/HLA-CDS.fa - | $root/bwa mem -aD.1 -t2 $pre.tmp - 2>/dev/null | gzip -1 > $pre.sam.gz
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echo "** Typing..." >&2
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$root/k8 $root/typeHLA.js $pre.sam.gz > $pre.gt
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# delete temporary files
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rm -f $pre.tmp.*
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[ $is_ctg -eq 1 ] && rm -f $pre.mag.gz
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