21 lines
411 B
Plaintext
21 lines
411 B
Plaintext
|
#!/bin/bash
|
||
|
|
|
||
|
|
ctg_opt=""
|
||
|
|
if [ $# -gt 1 ] && [ $1 == '-A' ]; then
|
||
|
|
ctg_opt="-A"
|
||
|
|
shift
|
||
|
|
fi
|
||
|
|
|
||
|
|
if [ $# -eq 0 ]; then
|
||
|
|
echo "Usage: $0 <prefix>"
|
||
|
|
exit 1
|
||
|
|
fi
|
||
|
|
|
||
|
|
for f in $1.HLA-*.fq; do
|
||
|
|
gene=`echo $f | perl -pe 's/^.*(HLA-[A-Z]+[0-9]*).*fq$/$1/'`
|
||
|
|
echo -e "\n*** Processing gene $gene...\n" >&2
|
||
|
|
`dirname $0`/typeHLA.sh $ctg_opt $1 $gene
|
||
|
|
done
|
||
|
|
|
||
|
|
ls $1.HLA-*.gt | xargs -i echo grep ^GT {} \| head -1 | sh | sed "s,^GT,$1,"
|