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extractAlltoFast.sh
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extractAlltoFast.sh
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#!/bin/bash
#
# extractAlltoFast.sh
#
# retrieve FASTA or FASTQ records (parent file) from an input file that's either BLASTn (m8 table, sam file, or list of headers); FASTA; FASTQ
# Chiu Laboratory
# University of California, San Francisco
# January, 2014
#
# --- uses the C program "fqextract.c" (http://www.biostars.org/p/10353/) ---
#
# Copyright (C) 2014 Samia Naccache - All Rights Reserved
# SURPI has been released under a modified BSD license.
# Please see license file for details.
# Last revised 5/19/2014
if [ $# -lt 6 ]
then
echo "<inputfile> <Input File Type [BLASTN/FASTA/FASTQ]> <Parent file> <Parent File Type [FASTA/FASTQ]> <Output file> <Output format: [FASTA/FASTQ]>"
exit 65
fi
###
inputfile=$1
inputfile_type=$2
parentfile=$3
parentfile_type=$4
outputfile=$5
output_format=$6
###
scriptname=${0##*/}
echo -e "$(date)\t$scriptname\tprepare $inputfile_type file"
if [ $inputfile_type = BLASTN ]
then
awk '{print$1}' $inputfile > $inputfile.header
echo -e "$(date)\t$scriptname\tuniqued blastn file, replaced beginning with @"
if [ $parentfile_type = FASTA ]
then
seqtk subseq $parentfile $inputfile.header > $outputfile
elif [ $parentfile_type = FASTQ ]
then
if [ $output_format = FASTQ]
then
cat $parentfile | fqextract $inputfile.header > $outputfile
elif [ $output_format = FASTA ]
then
cat $parentfile | fqextract $inputfile.header > $inputfile.ex.fq
sed "n;n;n;d" $inputfile.ex.fq | sed "n;n;d" | sed "s/^@/>/g" > $outputfile
rm -f $inputfile.ex.fq
fi
fi
rm -f $inputfile.header
elif [ $inputfile_type = FASTA ]
then
grep ">" $inputfile | sed 's/>//g' > $inputfile.header
echo -e "$(date)\t$scriptname\tDone preparing input Fasta file "
if [ $parentfile_type = FASTA ]
then
seqtk subseq $parentfile $inputfile.header > $outputfile
elif [ $parentfile_type = FASTQ ]
then
if [ $output_format = FASTQ ]
then
cat $parentfile | fqextract $inputfile.header > $outputfile
elif [ $output_format = FASTA ]
then
cat $parentfile | fqextract $inputfile.header > $inputfile.ex.fq
sed "n;n;n;d" $inputfile.ex.fq | sed "n;n;d" | sed "s/^@/>/g" > $outputfile
rm -f $inputfile.ex.fq
fi
fi
rm -f $inputfile.header
elif [ $inputfile_type = FASTQ ]
then
grep "^@" $inputfile | sed 's/@//g' > $inputfile.header
echo -e "$(date)\t$scriptname\tDone preparing input Fastq file"
if [ $parentfile_type = FASTA ]
then
seqtk subseq $parentfile $inputfile.header > $outputfile
elif [ $parentfile_type = FASTQ ]
then
if [ $output_format = FASTQ ]
then
cat $parentfile | fqextract $inputfile.header > $inputfile.ex.fq
elif [ $output_format = FASTA ]
then
cat $parentfile | fqextract $inputfile.header > $inputfile.ex.fq
sed "n;n;n;d" $inputfile.ex.fq | sed "n;n;d" | sed "s/^@/>/g" > $outputfile
rm -f $inputfile.ex.fq
fi
fi
rm -f $inputfile.header
fi