Revision d6501d6d78c65d29b415c9c8b96298d4d581f418 authored by Arjun Raj on 18 June 2014, 17:12:56 UTC, committed by Arjun Raj on 18 June 2014, 17:12:56 UTC
0 parent
unzipAndConcatenateZippedFasta.sh
#!/bin/bash
ZIPFILEDIRECTORY=$1
OUTFASTADIRECTORY=$2
for dirname in $ZIPFIELDIRECTORY/* ; do
cd $dirname
INPUT=`ls *001_R1*`
SAMPLE=`echo $INPUT | cut -d'_' -f 1`
if [ ! -d $EXPERIMENT/raw ]; then
mkdir $EXPERIMENT/raw
fi
if [ ! -d $EXPERIMENT/raw/$SAMPLE ]; then
mkdir $EXPERIMENT/raw/$SAMPLE
fi
for i in *.gz; do
gunzip -c $i > ${i%.*}
done
FASTQR1=`echo $SAMPLE'_R1.fastq'`
FASTQR2=`echo $SAMPLE'_R2.fastq'`
cat *R1*fastq > $EXPERIMENT/raw/$SAMPLE/$FASTQR1
cat *R2*fastq > $EXPERIMENT/raw/$SAMPLE/$FASTQR2
done
Computing file changes ...