Perl学习17之生信简单运用

"pythonic生物人"的第29篇分享。

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正文开始啦

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1、计算一条DNA序列中的ATGC个数GC含量格式化输出

• gccount_read.pl

#!/usr/bin/perl
use strict;
use warnings;
my $read = "AACAAACCCCTTTTCTCTATTAAAAAATACAAAATAGCTTAGCTGCGGCATAGTGGAGCACG";
my $G = ($read =~ s/G/G/g);#s为匹配表示匹配,($read =~ s/G/G/g)返回匹配次数个数
my $C = ($read =~ s/C/C/g);
my $A = ($read =~ s/A/A/g);
my $T = ($read =~ s/T/T/g);
my $total = $G + $C + $A +$T;
my $GC_P = ($G + $C)/$total;

#格式化输出printf
printf "\$G:%d\n\$C:%d\n\$A:%d\n\$T:%d\n\$total:%d\n\$GC_P:%.2f\n",($G,$C,$A,$T,$total,$GC_P);

#sprintf格式化不输出
my $result = sprintf("\$G:%d\n\$C:%d\n\$A:%d\n\$T:%d\n\$total:%d\n\$GC_P:%.2f\n",($G,$C,$A,$T,$total,$GC_P));

#输出到文件GC.file
open OUT,">","./GC.file";
print OUT $result;
close OUT;

• perl gccount_read.pl

$G:10

$C:14

$A:23

$T:15

$total:62

$GC_P:0.39 

cat GC.file

$G:10

$C:14

$A:23

$T:15

$total:62

$GC_P:0.39

2、每一行数据求和，每个数使用各自行和归一化

输入文件：sumfile

a       1       2       3       4       5       6

b       1       2       3       4       5       6

目的：分别求a，b行中所有数之和，每个数在该行所占比例格式化输出

脚本：sum1.pl

#!/usr/bin/perl
use strict;
use warnings;
 
open IN,"./sumfile";
while(<IN>){
        chomp;
        my @t=split;
        my $sum=0;
 
        for my $i (1..5){
                $sum+=$t[$i];
        }
        print "$t[0]\t$sum\t";#求和
 
        for my $i (1..5){
                my $percent=$t[$i]/$sum;
                printf "%.2f\t","$percent";
        }
        print "\n";#换行
 
                  }

perl sum1.pl

a 15 0.07 0.13 0.20 0.27 0.33

b 15 0.07 0.13 0.20 0.27 0.33

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