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Perl-添加下划线并对行进行排序

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Perl-添加下划线并对行进行排序

由于我是生物学家并且是 Perl 新手，我希望得到 Perl 专家的帮助

猫输入.txt

##gff-version 2
##source-version geneious 5.6.3
gi371443188gbJH5566721_extraction_reversed  Geneious    CDS 1043    1132    .    +   .   Name=Xm ITGB3;created by=User;modified by=User;ID=Pa0FVoXpt/GgL1I/VO7LY0UlFAc.1341246976743.1
gi371443188gbJH5566721_extraction_reversed  Geneious    CDS 2063    2260    .    +   .   Name=Xm ITGB3;created by=User;modified by=User;ID=Pa0FVoXpt/GgL1I/VO7LY0UlFAc.1341246976743.1
gi371443188gbJH5566721_extraction_reversed  Geneious    CDS 2336    2593    .    +   .   Name=Xm ITGB3;created by=User;modified by=User;ID=Pa0FVoXpt/GgL1I/VO7LY0UlFAc.1341246976743.1
gi371443188gbJH5566721_extraction_reversed  Geneious    CDS 3474    3633    .    +   .   Name=Xm ITGB3;created by=User;modified by=User;ID=Pa0FVoXpt/GgL1I/VO7LY0UlFAc.1341246976743.1
gi371443188gbJH5566721_extraction_reversed  Geneious    extracted region    1   13933   .   +   .   Name=Extracted region from gi|371443188|gb|JH556672.1|;Extracted interval="2010140 <- 2024072"

我的输出.txt

gi371443188gbJH5566721_extraction_reversed  CDS 2023029 2022940 .    -   .   Name=Xm ITGB3;created by=User;modified by=User;ID=Pa0FVoXpt/GgL1I/VO7LY0UlFAc.1341246976743.1
gi371443188gbJH5566721_extraction_reversed  CDS 2022009 2021812 .    -   .   Name=Xm ITGB3;created by=User;modified by=User;ID=Pa0FVoXpt/GgL1I/VO7LY0UlFAc.1341246976743.1
gi371443188gbJH5566721_extraction_reversed  CDS 2021736 2021479 .    -   .   Name=Xm ITGB3;created by=User;modified by=User;ID=Pa0FVoXpt/GgL1I/VO7LY0UlFAc.1341246976743.1
gi371443188gbJH5566721_extraction_reversed  CDS 2020598 2020439 .    -   .   Name=Xm ITGB3;created by=User;modified by=User;ID=Pa0FVoXpt/GgL1I/VO7LY0UlFAc.1341246976743.1
###

我的预期输出

gi_371443188_gb_JH5566721  gene    2020598 2023029 .     -   .   Name=Xm ITGB3;created by=User;modified by=User;ID=Pa0FVoXpt/GgL1I/VO7LY0UlFAc.13412469767431
gi_371443188_gb_JH5566721   CDS 2020598 2020439 .    -   .   Name=Xm ITGB3;created by=User;modified by=User;ID=Pa0FVoXpt/GgL1I/VO7LY0UlFAc.1341246976743.1
gi_371443188_gb_JH5566721   CDS 2021736 2021479 .    -   .   Name=Xm ITGB3;created by=User;modified by=User;ID=Pa0FVoXpt/GgL1I/VO7LY0UlFAc.1341246976743.1
gi_371443188_gb_JH5566721   CDS 2022009 2021812 .    -   .   Name=Xm ITGB3;created by=User;modified by=User;ID=Pa0FVoXpt/GgL1I/VO7LY0UlFAc.1341246976743.1
gi_371443188_gb_JH5566721   CDS 2023029 2022940 .    -   .   Name=Xm ITGB3;created by=User;modified by=User;ID=Pa0FVoXpt/GgL1I/VO7LY0UlFAc.1341246976743.1
###

我需要 Perl 专家的帮助来重新格式化下面给出的 Perl 代码中的输出。

1.我想在输出中将分数添加到数组[0]（即gi371443188gbJH5566721_extraction_reversed为gi_371443188_gb_JH5566721）

2.根据输出的第3列和第4列的值按升序对CDS的行进行排序（参见预期输出）

3.在文件顶部添加新行作为 gi_371443188_gb_JH556672.1 基因，其中包含 CDS 行的最小值和最大值（参见预期输出）

我的 Perl 代码如下。

#usr/bin/perl;

open(FH,"$ARGV[0]");

my %num="";
my %all="";
while(<FH>){
 chomp $_; 
   my @array=split("\t"); #print "$array[2]\n";
   if($array[2] eq "extracted region"){ 
   $array[8]=~/.*\w+=\"\d+ <- (\d+)"/gm; 
   $num{$array[0]}="$1";
   }
   if($array[2] eq "CDS"){
   $all{$array[0]}.="$_\n";
    }
    }

   foreach $i (keys %all){

    my @line=split "\n",$all{$i};
    for ($j=0;$j<=$#line;$j++){
    my @new_line=split "\t",$line[$j];
    my $pos1=$num{$i}-$new_line[3];
    my $pos2=$num{$i}-$new_line[4]; #print $num{$i}; exit;
    $new_line[6] =~ s/\+/-/g;
    print "$new_line[0]\t$new_line[2]\t$pos1\t$pos2\t$new_line[5]\t$new_line[6]\t$new_line[7]\t$new_line[8]\n";
    }
    }
    print "###\n";

答案1

这将做到这一点（即，我的输出与你的相匹配），尽管它不是最干净的。

用于添加下划线的正则表达式可能可以组合起来。但对于排序，您需要将所有输出行推送到一个列表，然后对其进行排序（也可以在传入端完成，但您仍然需要首先将所有输出行放在一个位置）。

--- test.pl~    2012-07-13 12:04:36.000000000 -0700
+++ test.pl 2012-07-13 12:17:58.000000000 -0700
@@ -1,4 +1,4 @@
-#usr/bin/perl
+#!/usr/bin/perl
 use strict;

 open(FH,"$ARGV[0]");
@@ -18,6 +18,7 @@
     }

    my $i;
+   my @output;
    foreach $i (keys %all){

     my @line=split "\n",$all{$i};
@@ -27,8 +28,15 @@
     my $pos1=$num{$i}-$new_line[3];
     my $pos2=$num{$i}-$new_line[4]; #print $num{$i}; exit;
     $new_line[6] =~ s/\+/-/g;
-    print "$new_line[0]\t$new_line[2]\t$pos1\t$pos2\t$new_line[5]\t$new_line[6]\t$new_line[7]\t$new_line[8]\n";
+    $new_line[0] =~ s/gi/gi_/;
+    $new_line[0] =~ s/gb/_gb_/;
+    $new_line[0] =~ s/_extraction_reversed//;
+    push @output, "$new_line[0]\t$new_line[2]\t$pos1\t$pos2\t$new_line[5]\t$new_line[6]\t$new_line[7]\t$new_line[8]\n";
     }
     }
+    @output = sort (@output);
+    foreach my $out (@output) {
+    print $out;
+    }
     print "###\n";

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