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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";
#!/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"; }

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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