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numt.sh
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numt.sh
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#!/bin/bash
###################################
# Author: Xiaoyu Zhou
# Email: xyzh@biomed.au.dk
###################################
function readfile() {
for file in `ls $1/*.fna`
do
if [ -f $1"/"$file ];then
#echo $1"/"$file
name=`basename $file`
tag=${name%.fna}
specie=${name%_*.fna}
typeset -l specie
#`perl cut.pl $tag`
#echo "$tag"
db="blast/"$tag"_nu.txt"
q="blast/"$tag"_mt.txt"
p="blast/"$tag"_pt.txt"
#echo "$db"
#echo "$q"
if [ -s $db ];then
if [ -s $q ];then
#`mv $db $q /home/zhouxy/CCDB/NUMT/`
#`/home/zhouxy/RepeatMasker/RepeatMasker -parallel 10 -species $specie -html -gff -dir repeat $name > log 2>> err`
#echo "$tag RepeatMasker Done"
blastn="blast/"$tag"_blastn.txt"
reblastn="blast/"$tag"_reblastn.txt"
#`cd /home/zhouxy/CCDB/fna/blast/`
# `~/ncbi-blast-2.6.0+/bin/makeblastdb -in $db -dbtype nucl`
#`cd /home/zhouxy/CCDB/fna/blast/`
# `~/ncbi-blast-2.6.0+/bin/blastn -db $db -query $q -out $blastn -word_size 11 -evalue 0.0001 -outfmt 7 -gapopen 5 -gapextend 2 -penalty -3 -reward 2 `
# echo "$tag BLAST Done"
#`cd /home/zhouxy/CCDB/fna/blast/`
# `~/ncbi-blast-2.6.0+/bin/makeblastdb -in $q -dbtype nucl`
#`cd /home/zhouxy/CCDB/fna/blast/`
# `~/ncbi-blast-2.6.0+/bin/blastn -db $q -query $db -out $reblastn -word_size 11 -evalue 0.0001 -outfmt 7 -gapopen 5 -gapextend 2 -penalty -3 -reward 2 `
#`cd /home/zhouxy/CCDB/fna/blast/`
# `mv $blastn $reblastn /home/zhouxy/CCDB/NUMT/blast_result/`
# echo "$tag REBLAST and Move Done"
#`cd /home/zhouxy/CCDB|perl data.pl $tag >log 2>>err`
#echo "$tag ALL DONE"
`perl numt.pl $tag`
echo "perl numt.pl $tag Done"
fi
fi
#if [ -s $q ];then
# if [ -s $p ];then
#`mv $db $q /home/zhouxy/CCDB/NUMT/`
#`/home/zhouxy/RepeatMasker/RepeatMasker -parallel 10 -species $specie -html -gff -dir repeat $name > log 2>> err`
#echo "$tag RepeatMasker Done"
# blastn_ptmt="blast/"$tag"_blastn_ptmt.txt"
# reblastn_ptmt="blast/"$tag"_reblastn_ptmt.txt"
#`cd /home/zhouxy/CCDB/fna/blast/`
# `~/ncbi-blast-2.6.0+/bin/makeblastdb -in $q -dbtype nucl`
#`cd /home/zhouxy/CCDB/fna/blast/`
# `~/ncbi-blast-2.6.0+/bin/blastn -db $q -query $p -out $blastn_ptmt -word_size 11 -evalue 0.0001 -outfmt 7 -gapopen 5 -gapextend 2 -penalty -3 -reward 2 `
# echo "ptmt $tag BLAST Done"
#`cd /home/zhouxy/CCDB/fna/blast/`
# `~/ncbi-blast-2.6.0+/bin/makeblastdb -in $p -dbtype nucl`
#`cd /home/zhouxy/CCDB/fna/blast/`
# `~/ncbi-blast-2.6.0+/bin/blastn -db $p -query $q -out $reblastn_ptmt -word_size 11 -evalue 0.0001 -outfmt 7 -gapopen 5 -gapextend 2 -penalty -3 -reward 2 `
#`cd /home/zhouxy/CCDB/fna/blast/`
# `mv $blastn_ptmt $reblastn_ptmt /home/zhouxy/CCDB/NUMT/blast_result/`
# echo "ptmt $tag REBLAST and Move Done"
#`cd /home/zhouxy/CCDB|perl data.pl $tag >log 2>>err`
#echo "$tag ALL DONE"
#`perl ptmp.pl $tag`
#echo "perl numt.pl $tag Done"
# fi
#fi
fi
done
}
#read -p "Please input the directory or file you want to their raed name:" n;
[ $# -eq 0 ] && { echo "Usage: $0 file path"; exit 1; }
#folder="./test"
readfile $1