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#!/bin/sh
if [ $# != 1 ] ; then
cat <<EOT
Usage: `basename $0` <dir_with_sequence_pairs>
This script seeks a directory for paired-end reads and processes
all pairs through seqsero using -m2 option. If a sequence pair
was processed before it will be skipped.
EOT
exit
fi
if [ ! -d $1 ] ; then
echo "$1 needs to be a directory"
exit
fi
numR1=`ls $1/*_R1_001.fastq.gz 2>/dev/null | wc -l`
if [ $numR1 -eq 0 ] ; then
echo "No sequences found in directory $1"
exit
fi
numR2=`ls $1/*_R2_001.fastq.gz | wc -l`
if [ $numR1 -ne $numR2 ] ; then
cat <<EOT
Warning: suspicious number of sequences R1=$numR1 and R2=$numR2
Both values should be equal. Please check that are data are valid.
Continuing processing anyway trying to find matching pairs.
EOT
fi
cd $1
for seq1 in `ls *_R1_001.fastq.gz` ; do
seq2=`echo $seq1 | sed 's/_R1_001\.fastq\.gz$/_R2_001.fastq.gz/'`
if [ ! -e "$seq2" ] ; then
echo "No matching sequence found for $seq1. File $seq2 does not exist."
else
check_old_results=`grep "^Input files:[[:space:]]\+\+$seq1 $seq2$" SeqSero_result*/Seqsero_result.txt`
if [ "$check_old_results" != "" ] ; then
echo "Calculation for $seq1 was done previously and can be found in `echo $check_old_results | sed 's/:Input files.*//'`"
else
seqsero -m 2 -i "$seq1" "$seq2"
fi
fi
done
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