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GCAtools.sh
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219 lines (173 loc) · 6.51 KB
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#!/usr/bin/env bash
# GCAtools
# Copyright (C) Yumin Huang
# Contact: [email protected]
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
set -e
if [ -z "$1" ]; then
echo "The arguments is empty!"
exit 1
fi
gettime() {
echo -e `date '+%Y-%m-%d %H:%M:%S ... '`
}
dont_stat_chromosome_group=""
stat_confidence=""
count_collinearity=""
Usage () {
echo ""
echo "GCAtools"
echo "Usage: GCAtools -f <clusterfolder> [options]"
echo ""
echo "Description:"
echo " Core workflow of GCAtools"
echo ""
echo "Options:"
echo " -h Show this message and exit"
#echo " -l <str> Prefix name of first file"
echo " -f <dir> Folder of cluster files"
echo " -t <str> Type of cluster files (dna or pep) [default dna]"
echo " -d <dir> Output file in <dir> [default ./GCAout]"
echo " -n <int> Number of threads [default 36]"
echo ""
echo "Author: Yumin Huang; [email protected]"
echo ""
exit 1
}
while getopts "hf:t:d:rcs:e:n:b:m" opt
do
case $opt in
h)
Usage
exit 1
;;
f)
fname=$OPTARG
;;
t)
ty=$OPTARG
;;
d)
directory=$OPTARG
;;
r)
dont_stat_chromosome_group="-r"
;;
c)
stat_confidence="-c"
;;
s)
fa_str=$OPTARG
;;
e)
evalue=$OPTARG
;;
n)
num_threads=$OPTARG
;;
b)
score_threshold=$OPTARG
;;
m)
count_collinearity="-m"
;;
?)
echo "Unknow argument!"
exit 1
;;
esac
done
logo () {
echo ""
echo " ==============================="
echo " || ||"
echo " || GCAtools ||"
echo " || Version: v0.0.1 ||"
echo " || ||"
echo " ==============================="
echo ""
}
logo
script_dir=$(dirname "$(realpath "${BASH_SOURCE[0]}")")
based=$(echo ${directory-./GCAout})
rm -rf ${based}
echo "Total $(ls "${fname}"|wc -l) fasta files detected in ${fname}..."
echo `gettime`"generate MSA..."
mkdir -p ${based}/msas/
mkdir -p ${based}/logs/
ls -1 $fname | parallel --joblog ${based}/logs/parallel.msa -j ${num_threads-36} ''"${script_dir}"'/bin/muscle-linux-x86.v5.2 -align '"${fname}"'/{} -output '"${based}/msas/{}"'' 2>${based}/logs/logs.msas || true
# 检查并报告 `parallel` 的退出状态
if [ $? -ne 0 ]; then
echo "Warning: parallel command failed."
fi
echo `gettime`"muscle MSA done..."
cp ${based}/logs/parallel.msa ${based}/logs/parallel.rawmsa
rd=1
while true; do
failed_count=$(awk '$7 != 0 || $8 != 0' <(tail -n+2 "${based}/logs/parallel.msa") | wc -l)
if [ "$failed_count" -eq 0 ]; then
echo "All files successed in MSA processings..."
break
else
echo "Round ${rd}: Total ${failed_count} fasta files failed in muscle MSA processings..."
echo "Preformed MSA by MAFFT..."
awk '$7 != 0 || $8 != 0' ${based}/logs/parallel.msa | awk -F '\t' 'NR>1{print $9}'|awk '{print $(NF-2)}'|while read f; do basename=$(basename "$f"); echo "$basename";done | parallel --joblog ${based}/logs/parallel.mafft -j ${num_threads-36} 'file=$(basename {}); mafft --maxiterate 1000 --ep 0 --genafpair '"${fname}"'/${file} > '"${based}"'/msas/${file}' 2>>${based}/logs/logs.msas
cat ${based}/logs/parallel.msa ${based}/logs/parallel.mafft > ${based}/logs/parallel.rawmsa
mv ${based}/logs/parallel.mafft ${based}/logs/parallel.msa
((rd++))
#echo "All files successed in MSA processings..."
fi
done
rm ${based}/logs/parallel.msa
echo `gettime`"build graph..."
if [ "$ty" == "pep" ]; then
PanPA build_gfa -d ${based}/msas/ -c ${num_threads-36} -o ${based}/graphs
else
mkdir -p ${based}/graphs
ls ${based}/msas/ | parallel --joblog ${based}/logs/parallel.construct -j ${num_threads-36} 'ii=$(echo {} | sed "s/fasta/gfa/g"); '"${script_dir}"'/bin/vg construct -m 999999999 -M '"${based}"'/msas/{} | '"${script_dir}"'/bin/vg convert -f - > '"${based}"'/graphs/${ii}'
fi
echo `gettime`"calculate graph complexity..."
echo "id segments links arcs mrank totalseg avgseg s mdegree avgdegree" > ${based}/graphs.stat; for i in `ls ${based}/graphs/`;do gfatools stat ${based}/graphs/${i} | awk -F ': ' 'BEGIN{print "'$i'"}{print $2}'|xargs -n 10 |awk '{sub(/\.gfa$/, "", $1); print}' >> ${based}/graphs.stat;done 2>${based}/logs/gfatools.log
python3 ${script_dir}/scripts/parse_alignlen.py ${based}/msas/ ${based}/graphs.length
mkdir -p ${based}/bubble
python3 ${script_dir}/scripts/parse_bubble.py ${based}/graphs ${based}/bubble/graphs.bubble ${based}/bubble/graphs.bubble.log > ${based}/logs/logs.bubble
paste ${based}/graphs.stat ${based}/graphs.length <(awk '{sub(/\.gfa$/, "", $1); print}' ${based}/bubble/graphs.bubble) |sed 's/[[:space:]]\+/\t/g' | awk '{if($1==$11&&$1==$15){print}else{print "Error: Inconsistent values found in line " NR ": " $0;exit 1;}}' | cut -f1-10,12-14,16- > ${based}/graphs.combined
# 检查awk的退出状态，如果不为0则终止脚本
if [ $? -ne 0 ]; then
echo "Script terminated due to inconsistent values."
exit 1
fi
awk -F "\t" 'BEGIN { OFS="\t" }
function harmonic_series(n) {
if (n <= 0) return 0
sum = 0
for (i = 1; i <= n; i++) {
sum += 1 / i
}
return sum
}
NR == 1 {
print $0, "indicatorL", "indicatorB"
}
NR > 1 {
h = harmonic_series($13)
indicatorL = $3 / ($11 * h)
indicatorB = $17 / $11
print $0, indicatorL, indicatorB
}' ${based}/graphs.combined > ${based}/graphs.complexity.txt
echo "处理完成，结果已保存到 ${based}/graphs.complexity.txt"