十年的生信

1 类似着这样的写法

#!/usr/bin/perl -w
use strict;
use warnings;

my $usage=<<USAGE;
Usage:
    perl $0 inputfile
USAGE
if(@ARGV==0){die $usage};

my $file=$ARGV[0];

2 类似这样的写法

#!/usr/bin/perl -w
use strict;
use warnings;
use Getopt::Long;
use POSIX;


my ($input,$output_dir,$seq_num,$file_num,$help,@libfiles);
GetOptions(
    "i:s" => \$input,
    "o:s" => \$output_dir,
    "n:i" => \$seq_num,
    "m:i" => \$file_num,
    "h:s" => \$help,
    "library=s" => \@libfiles
);

die `pod2text $0` if ((!$input) or (!$output_dir));

#帮助文档
=head1 Description

    This script is used to split fasta file, which is too large with thousangs of sequences;

=head1 Usage

    $0 -i <input> -o <outpu_dir> [-n <seq_num_per_file>] [-m <output_file_num>] -h --library lib/stdlib --library lib/extlib

=head1 Parameters

    -i  [str]   Input raw fasta file
    -o  [str]   Output file to which directory
    -n  [int]   Sequence number perl file, alternate chose paramerter 
    -m  [int]   Output file number (default:100)
    -h  [str]   Help manual
    --library   [dir]   Directory with multiple values

=cut

# !     代表否定
# s 代表字符串
# i     代表整型
# f     代表浮点数
#--library 用于传多个参数


print $input,"\n";
print $output_dir,"\n";
print $seq_num,"\n";
print $file_num,"\n";
@libfiles = split(/,/,join(',',@libfiles));
for my $i (0..$#libfiles){
    print $libfiles[$i],"\n";
}

参考：
perl进阶笔记
perlcoc

# 直接看图片，更好理解
-a 自动分隔模式，用空格分隔$并保存在@F中，也就是@F=split //, $
-F 指定-a的分隔符
-l 对输入的内容进行自动chomp，对输出的内容自动加换行符
-n 相当于while(<>)
-e 执行命令，也就是脚本
-p 自动循环+输出，也就是while(<>){命令（脚本）; print;}

cp /etc/passwd .
perl -pe 's/sshd/SSHD/g' passwd
perl -F':' -alne '/sshd/ && print $F[0]' passwd  | sed 's/sshd/SSHD/g'

grep -v "^$" passwd  | perl -alne 'print $a++." ".$_'
#类似于下面的这个
perl -e 'while(<>){chomp($_);if ($_ =~ /^\S/){print $a++." ".$_."\n"}}' passwd
#或
perl -ne 'print $a++." ".$_ if /\S/' passwd
#perl -e 'while(<>){if ($_ =~ /^\s/){print a."\n"}}' passwd

#输出匹配行的计数
perl -lne '$a++ if /^s/; END {print $a+0}' passwd

perl -MList::Util=sum -F':' -alne 'print sum @F' passwd

perl -alne '$t += @F; print $t' passwd
perl -alne '$t += @F; END{print $t}' passwd

perl -alne 'map{ /sshd/ && $t++ } @F; END{print $t}' passwd

perl -ne '/sshd/ && print' passwd

perl -ne 'print if /^\d+/' passwd

#矩阵转置
perl -MData::Dumper -e '@matrix=(["a","b","c","d"],["e","f","g","h"],["i","j","k","l"]);print Dumper (\ @matrix); @transposed=map{$x=$_;[map{$matrix[$_][$x]} 0..$#matrix];} 0..$#{$matrix[0]}; print Dumper(\ @transposed)'
#perl打印单引号
#单个单引号 
    perl -e 'print "'\''"'
#打印多个单引号 
perl -e 'print "'\'' '\''"'

可以用于多种perl的编程环境，让程序并行

#!/usr/bin/perl -w
#
use strict;
use warnings;
use threads;

my $j=0;
my $thread;

while(){
    while(scalar (threads -> list())<4){
        $j++;
        threads -> create(\&程序，参数...); 
    }
    for $thread(threads -> list(threads::all)){
        if ($thread -> is_joinable()){
            $thread -> join();
        }
    }
}

sub 自己的程序{
    ......
}

参考的网址： 1、Perl 中的线程 2、Perl多线程 3、perldoc:threads