当多年前的脚本莫名奇妙的运行，然后又莫名其妙的运行不起来，觉得我的天都踏了
使用脚本提取blast结果，需要两个perl模块，可以使用的环境，记录下，下次用的时候直接使用
perl find_insertion_point.pl NIP.bl 6
###find_insertion_point.pl
use strict;
use Bio::SearchIO;
use Bio::Search::Result::GenericResult;
my $file=$ARGV[0];
my $out=$ARGV[1];
my $in = new Bio::SearchIO(-format => 'blast',
-file => "$file");
open OUTFILE ,(">$out.bed");
#my ;
while( my $result = $in->next_result ) {
if ($result->num_hits<888) {
## $result is a Bio::Search::Result::ResultI compliant object
while( my $hit = $result->next_hit ) {
## $hit is a Bio::Search::Hit::HitI compliant object
while( my $hsp = $hit->next_hsp ) {
## $hsp is a Bio::Search::HSP::HSPI compliant object
#$insertion_number = $insertion_number + 1;
print OUTFILE $hit->name ;
# print OUTFILE "\t";
# print OUTFILE $hsp->start('hit');
# print OUTFILE "\t";
# print OUTFILE $hsp->end('hit');
# print OUTFILE "\t";
# print OUTFILE $result->query_name();
print OUTFILE "\n";
}
}
}
}
# .bashrc
# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
# Uncomment the following line if you don't like systemctl's auto-paging feature:
# export SYSTEMD_PAGER=
alias le='less -mSN'
alias les='less -SN'
alias ls='ls --color=auto'
alias l='ls -alrth'
alias l.='ls -d .* --color=auto'
alias lh='ls -ltrh'
alias ll='ls -l --time-style=+"%Y-%m-%d %H:%M:%S" --color=auto'
alias lll='ls -alrht --time-style=full-iso --color=auto'
# User specific aliases and functions
#Appreance
GREEN="\[\e[32;1m\]"
BLUE="\[\e[36;1m\]"
WHITE="\[\e[37;1m\]"
BLACK="\[\e[30;1m\]"
RED="\[\e[31;1m\]"
YELLOW="\[\e[33;1m\]"
PURPLE="\[\e[35;1m\]"
DARK_GREEN="\[\e[36;1m\]"
CLEAR="\[\e[0m\]"
_JOB_="Jobs: \j"
_FILECOUNT_="Files: $(/bin/ls -1 | /usr/bin/wc -l | /bin/sed 's: ::g')"
_FACE_="\`if [ $= 0 ]; then echo \[\e[1\;35m\]^_^\[\e[0m\]; else echo \[\e[1\;31m\]\>_\<\[\e[0m\]; fi\`"
_HISTORY_="\!"
_DATE_="$(/bin/date)"
_CLOCK_="\t"
_SIZE_="Size: $(/bin/ls -lah | /usr/bin/head -n 1 | /usr/bin/cut -d ' ' -f 2)"
_PATH_="$(pwd)"
export PS1="${YELLOW} \H $BLUE||$RED \u $BLUE||$WHITE \d \A $BLUE||$GREEN $_PATH_ \n${BLUE}\$> $CLEAR"
export PATH=$PATH:/public/home/fengting/data/wild/sratoolkit.2.8.2-ubuntu64/
eval "$(perl -I$HOME/opt/lib/perl5 -Mlocal::lib=$HOME/opt)"
alias cpanm="cpanm --mirror http://mirrors.163.com/cpan --mirror-only"
export PERL5LIB=/public/home/fengting/miniconda3/envs/annotation/lib/5.26.2:$PERL5LIB
export PERL5LIB=/public/home/fengting/miniconda3/pkgs/perl-bioperl-1.6.924-4/lib/perl5/site_perl/5.22.0
export PATH=$PATH:/public/home/fengting/miniconda3/envs/annotation/share/gmes_linux_64/gmes_petap.pl>>~/.bashrc
export PERL5LIB=/public/home/fengting/.cpan/build/YAML-1.30-0/blib/lib/YAML
export PERL5LIB=/public/home/fengting/conda/lib/5.26.2/CPAN/Meta/YAML.pm
export PERL5LIB=/public/home/fengting/.cpan/Metadata
export PERL5LIB=/public/home/fengting/miniconda3/lib/site_perl/5.26.2
export PERL5LIB=/usr/share/perl5/lib/perl5:$PERL5LIB
export PERL5LIB=/public/home/fengting/miniconda3/pkgs/perl-bioperl-1.6.924-4/lib/perl5/site_perl/5.22.0/:$PERL5LIB
export PATH=$PATH:/public/home/fengting/data/wild/sratoolkit.2.8.2-ubuntu64/
eval "$(perl -I$HOME/opt/lib/perl5 -Mlocal::lib=$HOME/opt)"
alias cpanm="cpanm --mirror http://mirrors.163.com/cpan --mirror-only"
export PERL5LIB=/public/home/fengting/miniconda3/envs/annotation/lib/5.26.2:$PERL5LIB
export PERL5LIB=/public/home/fengting/miniconda3/pkgs/perl-bioperl-1.6.924-4/lib/perl5/site_perl/5.22.0
export PATH=$PATH:/public/home/fengting/miniconda3/envs/annotation/share/gmes_linux_64/gmes_petap.pl>>~/.bashrc
gatk
export PATH="/public/home/lianglunping/conda/software/gatk-4.0.0.0:$PATH"
export PATH=/public/home/lianglunping/conda/software/gatk-4.1.0.0:/public/home/lianglunping/conda/condabin:/public/home/lianglunping/.aspera/connect/bin:/public/home/lianglunping/.aspera/connect/bin:/public/home/lianglunping/bin:/public/home/lianglunping/conda3/bin:/opt/clusconf/sbin:/opt/clusconf/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/public/software/bin:/public/home/lianglunping/conda/bin
eupan
export PATH=$PATH:/public/home/fengting/demo/pan111/EUPAN/EUPAN-v0.44/bin:
export LD_PATH=$LD_PATH:/public/home/fengting/demo/pan111/EUPAN/EUPAN-v0.44/lib:
export PERL5LIB=$PERL5LIB:/public/home/fengting/demo/pan111/EUPAN/EUPAN-v0.44/lib:
source /public/home/fengting/demo/pan111/EUPAN/EUPAN-v0.44/bin/eupan_cmd.sh
先运行着，以后不要瞎改环境，不然重新调试环境很麻烦