42 lines
1.3 KiB
Bash
Executable File
42 lines
1.3 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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root=`dirname $0`
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pre=$1.$2
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# de novo assembly
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if [ $is_ctg -eq 0 ]; then
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len=`$root/seqtk comp $pre.fq | awk '{++x;y+=$2}END{printf("%.0f\n", y/x)}'`
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$root/fermi2.pl unitig -t2 -l$len -p $pre.tmp $pre.fq > $pre.tmp.mak
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make -f $pre.tmp.mak EXE_FERMI2=$root/fermi2 EXE_ROPEBWT2=$root/ropebwt2
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else
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ln -sf $pre.fq $pre.tmp.mag.gz
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fi
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# get contigs overlapping HLA exons
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(ls $root/HLA-idx/*.fa | xargs -i $root/bwa mem -t2 -B1 -O1 -E1 {} $pre.tmp.mag.gz 2>/dev/null) | grep -v ^@ | sort -k3,3 -k4,4n | bgzip > $pre.tmp.sam.gz
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$root/tabix -Bpsam $pre.tmp.sam.gz $root/HLA-approx.anno | cut -f1 | sort | uniq > $pre.tmp.kept
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gzip -dc $pre.tmp.sam.gz | perl -ane 'print "$F[0]\n" if /AS:i:(\d+).*XS:i:(\d+)/&&$1==$2' | cut -f1 | sort | uniq > $pre.tmp.dropped
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awk -v f=$pre.tmp.dropped 'BEGIN{while((getline<f)>0)l[$1]=1}!l[$1]' $pre.tmp.kept | $root/seqtk subseq $pre.tmp.mag.gz - | gzip -1 > $pre.tmp.fq.gz
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# map HLA exons to de novo contigs
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$root/bwa index -p $pre.tmp $pre.tmp.fq.gz 2> /dev/null
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$root/bwa mem -aD.1 -t2 $pre.tmp $root/hla.fa | egrep "^(@|$2)" > $pre.sam
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# type HLA
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$root/k8 $root/bwa-typeHLA.js $pre.sam > $pre.gt
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# delete temporary files
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rm -f $pre.tmp.*
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