Perl- Adding underscore and sorting rows

Question

As I am biologist and new to perl, I would like to get help of perl expert

cat input.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"

My output.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
###

My expected ouput

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
###

I would like help of perl expert in reformating my output in perl code given below.

1.I would like add under score to array[0] in output (i.e gi371443188gbJH5566721_extraction_reversed as gi_371443188_gb_JH5566721)

2.sort rows of CDS in ascending order based on values of column3 & 4 of the output (see expected output)

3.Add new row at the top of file as gi_371443188_gb_JH556672.1 gene with minimum & maximum value of CDS rows (see expected output)

My Perl code is given below.

#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";

Answer 1

This will do it (i.e., my output matches yours), although it's not quite the cleanest.

The regexp's for adding the underscores can probably be combined. But for the sorting, you need to push all of your output lines to a list and then sort it (it could also be done on the incoming side, but you still need all of it in one place first).

--- 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";