polished the run script

gt1 · Nov 3, 2014 · 4cbb0cb · 4cbb0cb
1 parent 9dbf152
commit 4cbb0cb
Showing 1 changed file with 17 additions and 8 deletions.
diff --git a/bwa-typeHLA.sh b/bwa-typeHLA.sh
@@ -9,11 +9,20 @@ root=`dirname $0`
 pre=$1.$2
 len=`$root/seqtk comp $pre.fq | awk '{++x;y+=$2}END{printf("%.0f\n", y/x)}'`
 
-$root/fermi2.pl unitig -t2 -l$len -p $pre.utg $pre.fq > $pre.utg.mak
-make -f $pre.utg.mak
-$root/bwa mem -B1 -O1 -E1 $root/HLA-ALT.fa $pre.utg.mag.gz | grep -v ^@ | sort -k3,3 -k4,4n | bgzip > $pre.utg.alt.gz
-$root/tabix -Bpsam $pre.utg.alt.gz $root/HLA-approx.anno | cut -f1 | sort | uniq | $root/seqtk subseq $pre.utg.mag.gz - | gzip -1 > $pre.utg.fq.gz
-rm $pre.utg.{flt,ec,raw,pre}.* $pre.utg.mag* $pre.utg.mak $pre.utg.alt.gz
-$root/bwa index -p $pre.utg $pre.utg.fq.gz
-$root/bwa mem -aD.1 -t2 $pre.utg $root/hla.fa | egrep "^(@|$2)" > $pre.utg.sam
-rm $pre.utg.{ann,amb,bwt,sa,pac}
+# de novo assembly
+$root/fermi2.pl unitig -t2 -l$len -p $pre.tmp $pre.fq > $pre.tmp.mak
+make -f $pre.tmp.mak
+
+# get contigs overlapping HLA exons
+$root/bwa mem -B1 -O1 -E1 $root/HLA-ALT.fa $pre.tmp.mag.gz | grep -v ^@ | sort -k3,3 -k4,4n | bgzip > $pre.tmp.alt.gz
+$root/tabix -Bpsam $pre.tmp.alt.gz $root/HLA-approx.anno | cut -f1 | sort | uniq | $root/seqtk subseq $pre.tmp.mag.gz - | gzip -1 > $pre.tmp.fq.gz
+
+# map HLA exons to de novo contigs
+$root/bwa index -p $pre.tmp $pre.tmp.fq.gz
+$root/bwa mem -aD.1 -t2 $pre.tmp $root/hla.fa | egrep "^(@|$2)" > $pre.tmp.sam
+
+# type
+$root/k8 $root/bwa-typeHLA.js $pre.tmp.sam > $pre.gt
+
+# delete temporary files
+rm -f $pre.tmp.*