comment on

Remember I am new at Perl, so my approach is probably pretty brutish.

Input:

==> igenome.genes.onlyexons.uniq.gtf <==
chr1    unknown    exon1    815    4692    .    -    .    gene_id "LOC
+653635"; gene_name "LOC653635"; transcript_id "XR_017611.2"; tss_id "
+TSS10265";
chr1    unknown    exon2    4833    4901    .    -    .    gene_id "LO
+C653635"; gene_name "LOC653635"; transcript_id "XR_017611.2"; tss_id 
+"TSS10265";
chr1    unknown    exon3    5659    5810    .    -    .    gene_id "LO
+C653635"; gene_name "LOC653635"; transcript_id "XR_017611.2"; tss_id 
+"TSS10265";
chr1    unknown    exon4    6470    6628    .    -    .    gene_id "LO
+C653635"; gene_name "LOC653635"; transcript_id "XR_017611.2"; tss_id 
+"TSS10265";
chr1    unknown    exon5    6717    6918    .    -    .    gene_id "LO
+C653635"; gene_name "LOC653635"; transcript_id "XR_017611.2"; tss_id 
+"TSS10265";
chr1    unknown    exon6    7096    7231    .    -    .    gene_id "LO
+C653635"; gene_name "LOC653635"; transcript_id "XR_017611.2"; tss_id 
+"TSS10265";
chr1    unknown    exon7    7469    7605    .    -    .    gene_id "LO
+C653635"; gene_name "LOC653635"; transcript_id "XR_017611.2"; tss_id 
+"TSS10265";
chr1    unknown    exon8    7778    7924    .    -    .    gene_id "LO
+C653635"; gene_name "LOC653635"; transcript_id "XR_017611.2"; tss_id 
+"TSS10265";
chr1    unknown    exon9    8131    8229    .    -    .    gene_id "LO
+C653635"; gene_name "LOC653635"; transcript_id "XR_017611.2"; tss_id 
+"TSS10265";
chr1    unknown    exon10    8776    8938    .    -    .    gene_id "L
+OC653635"; gene_name "LOC653635"; transcript_id "XR_017611.2"; tss_id
+ "TSS10265";
chr1    unknown    exon11    14601    14754    .    -    .    gene_id 
+"LOC653635"; gene_name "LOC653635"; transcript_id "XR_017611.2"; tss_
+id "TSS10265";
chr1    unknown    exon12    19184    19919    .    -    .    gene_id 
+"LOC653635"; gene_name "LOC653635"; transcript_id "XR_017611.2"; tss_
+id "TSS10265";
chr1    unknown    exon13    58954    59871    .    +    .    gene_id 
+"OR4F5"; gene_name "OR4F5"; p_id "P1363"; transcript_id "NM_001005484
+.1"; tss_id "TSS13645";
chr1    unknown    exon14    77385    80096    .    +    .    gene_id 
+"LOC100132632"; gene_name "LOC100132632"; p_id "P27379"; transcript_i
+d "XM_001724183.1"; tss_id "TSS10177";
chr1    unknown    exon15    110381    110795    .    -    .    gene_i
+d "LOC643670"; gene_name "LOC643670"; transcript_id "XR_039242.1"; ts
+s_id "TSS5420";
chr1    unknown    exon16    114643    114701    .    -    .    gene_i
+d "LOC729737"; gene_name "LOC729737"; p_id "P4208"; transcript_id "XM
+_001133863.1"; tss_id "TSS9238";
chr1    unknown    exon17    118918    119086    .    -    .    gene_i
+d "LOC643670"; gene_name "LOC643670"; transcript_id "XR_039242.1"; ts
+s_id "TSS5420";
chr1    unknown    exon18    123237    130714    .    -    .    gene_i
+d "LOC643670"; gene_name "LOC643670"; transcript_id "XR_039242.1"; ts
+s_id "TSS5420";
chr1    unknown    exon19    123324    130714    .    -    .    gene_i
+d "LOC653340"; gene_name "LOC653340"; transcript_id "XR_039243.1"; ts
+s_id "TSS5420";
chr1    unknown    exon20    129326    129559    .    -    .    gene_i
+d "LOC729737"; gene_name "LOC729737"; p_id "P4208"; transcript_id "XM
+_001133863.1"; tss_id "TSS9238";
chr1    unknown    exon21    129653    129710    .    -    .    gene_i
+d "LOC729737"; gene_name "LOC729737"; p_id "P4208"; transcript_id "XM
+_001133863.1"; tss_id "TSS9238";
chr1    unknown    exon22    132810    132874    .    -    .    gene_i
+d "LOC729737"; gene_name "LOC729737"; p_id "P4208"; transcript_id "XM
+_001133863.1"; tss_id "TSS9238";
chr1    unknown    exon23    133719    134341    .    -    .    gene_i
+d "LOC729737"; gene_name "LOC729737"; p_id "P4208"; transcript_id "XM
+_001133863.1"; tss_id "TSS9238";
chr1    unknown    exon24    217633    218641    .    -    .    gene_i
+d "LOC728481"; gene_name "LOC728481"; transcript_id "XR_015292.2"; ts
+s_id "TSS13278";
chr1    unknown    exon25    313133    319752    .    +    .    gene_i
+d "LOC100132287"; gene_name "LOC100132287"; transcript_id "XR_039254.
+1"; tss_id "TSS18904";
[download]

 
#!/usr/bin/perl -w

use strict;

my $previous = '';
my $exon = 1;
while (<>) { 
  chomp;
  my(@gtf) = split; 

  chop($gtf[8] = join ":", @gtf[8,9]); 
  chop($gtf[10] = join ":", @gtf[10,11]);
  chop($gtf[12] = join ":", @gtf[12,13]);

# Restart exon# for different gene names
  if ( $gtf[9] ne $previous ) {
    $gtf[2] = 'exon1'; 
  } elsif ( $gtf[9] eq $previous ) {
    $exon =~ s/(\d+)/$1+1/e; 
  } 
  $previous = $gtf[9];
  $exon = $gtf[2];

  $gtf[8] = join "_", @gtf[8,10,12,2];
  my $bed = join "\t", @gtf[0,3,4,8];
  print "$bed\n";
}
[download]

Here's 25 lines of the output (I'll bold the lines where the problem appears and simplify the data for formatting by removing array items 10 and 12):

chr1 815 4692 gene_id:"LOC653635"_exon1

chr1 4833 4901 gene_id:"LOC653635"_exon2

chr1 5659 5810 gene_id:"LOC653635"_exon3

chr1 6470 6628 gene_id:"LOC653635"_exon4

chr1 6717 6918 gene_id:"LOC653635"_exon5

chr1 7096 7231 gene_id:"LOC653635"_exon6

chr1 7469 7605 gene_id:"LOC653635"_exon7

chr1 7778 7924 gene_id:"LOC653635"_exon8

chr1 8131 8229 gene_id:"LOC653635"_exon9

chr1 8776 8938 gene_id:"LOC653635"_exon10

chr1 14601 14754 gene_id:"LOC653635"_exon11

chr1 19184 19919 gene_id:"LOC653635"_exon12

chr1 58954 59871 gene_id:"OR4F5"_exon1

chr1 77385 80096 gene_id:"LOC100132632"_exon1

chr1 110381 110795 gene_id:"LOC643670"_exon1

chr1 114643 114701 gene_id:"LOC729737"_exon1

chr1 118918 119086 gene_id:"LOC643670"_exon1

chr1 123237 130714 gene_id:"LOC643670"_exon18

chr1 123324 130714 gene_id:"LOC653340"_exon1

chr1 129326 129559 gene_id:"LOC729737"_exon1

chr1 129653 129710 gene_id:"LOC729737"_exon21

chr1 132810 132874 gene_id:"LOC729737"_exon22

chr1 133719 134341 gene_id:"LOC729737"_exon23

chr1 217633 218641 gene_id:"LOC728481"_exon1

chr1 313133 319752 gene_id:"LOC100132287"_exon1

The bolded lines should count up from 1, for example, "exon18" should read "exon2" and exon21, exon 22, exon23 should read exon2, exon3, exon4.

In reply to Re^7: Comparing adjacent lines by daccame
in thread Comparing adjacent lines by daccame

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