/
assembly.functions.sh
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/
assembly.functions.sh
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#!/bin/bash
# scripts to reproduce the analysis and figures from Garrido-Oter et al., 2018
#
# originally by Ruben Garrido-Oter
# garridoo@mpipz.mpg.de
log() {
echo $(date -u)": "$1 >> $logfile
}
config () {
# parse arguments
local config_file=$1
# check config file
if [ ! -f $config_file ]
then
echo "invalid config file"
return 1
fi
# get dir and file paths
source $config_file
}
trim () {
# default parameters
local n_cores=$(nproc)
local lead=3
local trail=3
local sw_l=4
local sw_q=15
local min_l=36
local mode="PE"
# parse arguments
for i in "$@"
do
case $i in
-n_cores=* )
n_cores=`echo $i | sed 's/^.n_cores.//g'` ;;
-genome_id=* )
genome_id=`echo $i | sed 's/^.genome_id.//g'` ;;
-lead=* )
lead=`echo $i | sed 's/^.lead.//g'` ;;
-trail=* )
trail=`echo $i | sed 's/^.trail.//g'` ;;
-sw_l=* )
sw_l=`echo $i | sed 's/^.sw_l.//g'` ;;
-sw_q=* )
sw_q=`echo $i | sed 's/^.sw_q.//g'` ;;
-min_l=* )
min_l=`echo $i | sed 's/^.min_l.//g'` ;;
-mode=* )
mode=`echo $i | sed 's/^.mode.//g'` ;;
esac
done
if [[ (! -f $data_dir/"$genome_id"_1.fastq || ! -f $data_dir/"$genome_id"_2.fastq) && ! -f $data_dir/"$genome_id".fastq ]]
then
log "[genome "$genome_id"] fastq file not found!"
return 1
fi
rm -f $working_dir/"$genome_id"_forward_paired.fastq $working_dir/"$genome_id"_1_forward_unpaired.fastq \
$working_dir/"$genome_id"_reverse_paired.fastq $working_dir/"$genome_id"_2_reverse_unpaired.fastq
log "[genome "$genome_id"] trimming raw reads..."
if [ "$mode" = "PE" ]
then
java -jar $trim_path/trimmomatic-0.32.jar PE \
-threads $n_cores \
-phred33 $data_dir/"$genome_id"_1.fastq $data_dir/"$genome_id"_2.fastq \
$working_dir/"$genome_id"_forward_paired.fastq $working_dir/"$genome_id"_1_forward_unpaired.fastq \
$working_dir/"$genome_id"_reverse_paired.fastq $working_dir/"$genome_id"_2_reverse_unpaired.fastq \
MINLEN:$min_length \
ILLUMINACLIP:$trim_path/adapters/TruSeq3-PE-2.fa:2:40:15 \
LEADING:$lead \
TRAILING:$trail \
MINLEN:$min_length \
&>> $output
# SLIDINGWINDOW:$sw_length:$sw_min_q \
else if [ "$mode" = "SE" ]
then
java -jar $trim_path/trimmomatic-0.32.jar SE \
-threads $n_cores \
-phred33 $data_dir/"$genome_id".fastq \
$working_dir/"$genome_id".fastq \
MINLEN:$min_length \
ILLUMINACLIP:$trim_path/adapters/TruSeq3-SE.fa:2:40:15 \
LEADING:$lead \
TRAILING:$trail \
MINLEN:$min_length \
&>> $output
#SLIDINGWINDOW:$sw_length:$sw_min_q \
fi
fi
}
assemblyA5 () {
# default parameters
local n_cores=$(nproc)
# parse arguments
for i in "$@"
do
case $i in
-n_cores=* )
n_cores=`echo $i | sed 's/^.n_cores.//g'` ;;
-genome_id=* )
genome_id=`echo $i | sed 's/^.genome_id.//g'` ;;
esac
done
#~ # prepare folder for assembly file
log "[genome "$genome_id"] initializing assembly directory..."
local assembly_dir="$working_dir"/A5/"$genome_id"
if [ -d "$assembly_dir" ]
then
local ndatfiles=$(ls -A "$assembly_dir" | grep $genome_id | wc -l)
if [ $ndatfiles -gt 0 ]
then
log "[genome "$genome_id"] assembly folder is not empty!"
return 1
fi
else
mkdir -p $assembly_dir
fi
# run the assembler
log "[genome "$genome_id"] running A5 assembler..."
local dir=$PWD
cd $assembly_dir
a5_pipeline.pl --threads=$n_cores \
"$working_dir"/"$genome_id"_forward_paired.fastq \
"$working_dir"/"$genome_id"_reverse_paired.fastq \
$genome_id
cd $dir
}
assemblySOAP () {
# default parameters
local n_cores=$(nproc)
local max_rd_len=100
local avg_ins=200
local kmer=63
local mode="PE"
# parse arguments
for i in "$@"
do
case $i in
-n_cores=* )
n_cores=`echo $i | sed 's/^.n_cores.//g'` ;;
-genome_id=* )
genome_id=`echo $i | sed 's/^.genome_id.//g'` ;;
-max_rd_len=* )
max_rd_len=`echo $i | sed 's/^.max_rd_len.//g'` ;;
-avg_ins=* )
avg_ins=`echo $i | sed 's/^.avg_ins.//g'` ;;
-kmer=* )
kmer=`echo $i | sed 's/^.kmer.//g'` ;;
-mode=* )
mode=`echo $i | sed 's/^.mode.//g'` ;;
esac
done
# prepare folder for assembly file
log "[genome "$genome_id"] initializing assembly directory and creating config files..."
local assembly_dir="$working_dir"/SOAP/"$genome_id"
if [ -d "$assembly_dir" ]
then
local ndatfiles=$(ls -A "$assembly_dir" | grep $genome_id | wc -l)
if [ $ndatfiles -gt 0 ]
then
log "[genome "$genome_id"] assembly folder is not empty!"
return 1
fi
else
mkdir -p $assembly_dir
fi
# prepare config file
if [ "$mode" = "PE" ]
then
cat soap_template.config > $assembly_dir/"$genome_id".config
echo "q1="$working_dir"/"$genome_id"_forward_paired.fastq" >> $assembly_dir/"$genome_id".config
echo "q2="$working_dir"/"$genome_id"_reverse_paired.fastq" >> $assembly_dir/"$genome_id".config
echo "q="$working_dir"/"$genome_id"_1_forward_unpaired.fastq" >> $assembly_dir/"$genome_id".config
echo "q="$working_dir"/"$genome_id"_2_reverse_unpaired.fastq" >> $assembly_dir/"$genome_id".config
else if [ "$mode" = "SE" ]
then
cat soap_template.config > $assembly_dir/"$genome_id".config
echo "q="$working_dir"/"$genome_id".fastq" >> $assembly_dir/"$genome_id".config
fi
fi
sed -i "s/max_rd_len=/&"$max_rd_len"/g" $assembly_dir/"$genome_id".config
sed -i "s/avg_ins=/&$avg_ins/g" $assembly_dir/"$genome_id".config
# run the assembler
log "[genome "$genome_id"] running SOAP assembler..."
SOAPdenovo-63mer all -s $assembly_dir/"$genome_id".config \
-K $kmer -R -p $n_cores \
-o $assembly_dir/"$genome_id" \
&>$assembly_dir/"$genome_id".log
}
assemblyStats () {
local genome_id=$1
log "[genome "$genome_id"] generating assembly statistics..."
$PWD/assembly.stats.R $working_dir/SOAP/$genome_id/"$genome_id".scafSeq \
$genome_id \
$working_dir/SOAP \
"SOAP" \
&> $output
$PWD/assembly.stats.R $working_dir/A5/$genome_id/"$genome_id".final.scaffolds.fasta \
$genome_id \
$working_dir/A5 \
"A5" \
&> $output
}