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|
#!/bin/bash
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
# Matches reads by bowtie to genomes / sequences and throws out the reads that match.
function usage ()
{
echo "usage: $1 ( -a <single_file_with_all_reads.fastq[.gz] | -1 <first_reads.fastq[.gz]> -2 <second_reads.fastq[.gz]> [-u1 <first_unpaired.fastq[.gz]> -u2 <second_unpaired.fastq[.gz]>] ) -i <genome_index[,genome_index2,...]> [-o <output folder>] [-d <blast database>]"
}
function copy_if_not_same ()
{
if [ ! $1 -ef $2 ]
then
cp $1 $2
fi
}
function link_if_not_same ()
{
if [ ! $1 -ef $2 ]
then
ln -s $1 $2
fi
}
function clean_unpaired ()
{
echo "processing unpaired reads"
reads=$1
indices=$2
output_folder=$3
filename=$(basename $reads)
extension=${filename##*.}
targetfile="${output_folder}/${filename}"
if [ "$extension" = "gz" ]
then
copy_if_not_same $reads $targetfile
gunzip $targetfile
filename=${filename%.*}
extension=${filename##*.}
else
link_if_not_same $reads $targetfile
fi
myreads="${output_folder}/${filename}"
filename=${filename%.*}
cleanedreads="${output_folder}/${filename}_cleaned.${extension}"
mv $myreads $cleanedreads
readstmp=$cleanedreads.tmp
for i in "${indices[@]}"
do
echo "running bowtie on index $i"
bowtie -c -q -p 16 --suppress 6,7,8 $i $cleanedreads --un $readstmp > /dev/null 2> /dev/null
mv $readstmp $cleanedreads
done
}
function clean_paired ()
{
echo "processing paired reads"
left=$1
right=$2
indices=$3
output_folder=$4
path_to_script=$5
filename1=$(basename $left)
extension1=${filename1##*.}
if [ "$extension1" = "gz" ]
then
copy_if_not_same $left "${output_folder}/${filename1}"
gunzip "${output_folder}/${filename1}"
filename1=${filename1%.*}
extension1=${filename1##*.}
else
link_if_not_same $left "${output_folder}/${filename1}"
fi
myleft="${output_folder}/${filename1}"
filename1=${filename1%.*}
filename2=$(basename $right)
extension2=${filename2##*.}
if [ "$extension2" = "gz" ]
then
copy_if_not_same $right "${output_folder}/${filename2}"
gunzip "${output_folder}/${filename2}"
filename2=${filename2%.*}
extension2=${filename2##*.}
else
link_if_not_same $right "${output_folder}/${filename2}"
fi
myright="${output_folder}/${filename2}"
filename2=${filename2%.*}
cleanedleft="${output_folder}/${filename1}_cleaned.${extension1}"
filteredleft="${output_folder}/${filename1}_cleaned_filtered.${extension1}"
cleanedright="${output_folder}/${filename2}_cleaned.${extension2}"
filteredright="${output_folder}/${filename2}_cleaned_filtered.${extension2}"
mv $myleft $cleanedleft
mv $myright $cleanedright
timestamp=`date "+%m-%d_%T"`
for i in "${indices[@]}"
do
echo "running bowtie on index $i"
#bowtie -c -q -p 16 --suppress 6,7,8 --minins 0 --maxins 10000 --fr --tryhard $i -1 $cleanedleft -2 $cleanedright > paired_log.tmp 2> /dev/null
bowtie -c -q -p 16 --suppress 6,7,8 $i $cleanedleft > "${output_folder}/paired_log1_${timestamp}.tmp" 2> /dev/null
bowtie -c -q -p 16 --suppress 6,7,8 $i $cleanedright > "${output_folder}/paired_log2_${timestamp}.tmp" 2> /dev/null
echo "running filter_reads.py"
python3 ${path_to_script}/../reads_utils/filter/filter_reads.py $cleanedleft $cleanedright "${output_folder}/paired_log1_${timestamp}.tmp" "${output_folder}/paired_log2_${timestamp}.tmp"
mv $filteredleft $cleanedleft
mv $filteredright $cleanedright
done
rm "${output_folder}/paired_log1_${timestamp}.tmp" "${output_folder}/paired_log2_${timestamp}.tmp"
}
##### Main
left=
right=
left_unpaired=
right_unpaired=
indices=()
indexnames=()
all_reads=
script=$0
output_folder="."
blast_database="/acestorage/blast/db/nt"
scriptname=${script##*/}
path_to_script=${script%$scriptname}
while [ "$1" != "" ]; do
case $1 in
-a | --all_reads ) shift
all_reads=$1
;;
-1 | --first ) shift
left=$1
;;
-2 | --second ) shift
right=$1
;;
-u1 | --first_unpaired ) shift
left_unpaired=$1
;;
-u2 | --second_unpaired ) shift
right_unpaired=$1
;;
-o | --output ) shift
output_folder=$1
;;
-d | --database ) shift
blast_database=$1
;;
-i | --index ) shift
indexnames=$1
;;
-h | --help ) usage $script
exit
;;
* ) usage $script
exit 1
esac
shift
done
if [ -z "$left" -o -z "$right" ]
then
if [ -z "$all_reads" ]
then
usage $script
exit
fi
fi
if [ ${#indexnames[@]} -eq 0 ]
then
usage $script
exit
fi
dbname=${blast_database##*/}
path_to_db=${blast_database%$dbname}
mkdir -p $output_folder
old_IFS=${IFS}
IFS=","
for i in $indexnames #"${indexnames[@]}"
do
indices[$[${#indices[@]}]]="${path_to_db}/index/${i:0:2}/${i}"
if [ ! -e "${path_to_db}/index/${i:0:2}/${i}.1.ebwt" ]
then
echo "building index for sequence $i"
mkdir -p "${path_to_db}/index/${i:0:2}"
python3 ${path_to_script}/read_fasta_using_index.py $i "${blast_database}.fasta" > "${i}.fasta.tmp"
bowtie-build "${i}.fasta.tmp" "${path_to_db}/index/${i:0:2}/${i}"
rm "${i}.fasta.tmp"
fi
done
IFS=${old_IFS}
if [ "$all_reads" ]
then
echo "Splitting reads file into multiple files."
filename=$(basename $all_reads)
extension=${filename##*.}
if [ "$extension" = "gz" ]
then
cp $all_reads "${output_folder}/${filename}"
gunzip "${output_folder}/${filename}"
filename=${filename%.*}
extension=${filename##*.}
else
ln -s $all_reads "${output_folder}/${filename}"
fi
python3 ${path_to_script}/../reads_utils/conversion/split_any_fastq.py "${output_folder}/${filename}"
filename=${filename%.*}
left="${output_folder}/${filename}_left.${extension}"
right="${output_folder}/${filename}_right.${extension}"
left_unpaired="${output_folder}/${filename}_single_left.${extension}"
right_unpaired="${output_folder}/${filename}_single_right.${extension}"
fi
clean_paired $left $right $indices $output_folder $path_to_script
if [ "$left_unpaired" ]
then
clean_unpaired $left_unpaired $indices $output_folder
fi
if [ "$right_unpaired" ]
then
clean_unpaired $right_unpaired $indices $output_folder
fi
|
