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comparison PsiCLASS-1.0.2/ManipulateIntronFile.pl @ 0:903fc43d6227 draft default tip

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author lsong10
date Fri, 26 Mar 2021 16:52:45 +0000
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-1:000000000000 0:903fc43d6227
1 #!/usr/bin/env perl
2
3 use strict ;
4 use warnings ;
5
6 die "usage: a.pl intronA intronB [op]\n" if (@ARGV == 0 ) ;
7
8 my %intronInfo ;
9 my %chromRank ;
10
11 sub sortIntron
12 {
13 my @cols1 = split /\s+/, $a ;
14 my @cols2 = split /\s+/, $b ;
15
16 if ( $cols1[0] ne $cols2[0] )
17 {
18 $chromRank{ $cols1[0] } cmp $chromRank{ $cols2[0] } ;
19 }
20 elsif ( $cols1[1] != $cols2[1] )
21 {
22 $cols1[1] <=> $cols2[1] ;
23 }
24 else
25 {
26 $cols1[2] <=> $cols2[2] ;
27 }
28 }
29
30 open FP1, $ARGV[0] ;
31 my $cnt = 0 ;
32 while ( <FP1> )
33 {
34 chomp ;
35 my $line = $_ ;
36 my @cols = split /\s+/ ;
37 push @cols, 1 ;
38 @{ $intronInfo{ $cols[0]." ".$cols[1]." ".$cols[2] } } = @cols ;
39 if ( !defined $chromRank{ $cols[0]} )
40 {
41 $chromRank{ $cols[0] } = $cnt ;
42 ++$cnt ;
43 }
44 }
45 close FP1 ;
46
47 open FP1, $ARGV[1] ;
48 while ( <FP1> )
49 {
50 chomp ;
51 my $line = $_ ;
52 my @cols = split /\s+/ ;
53 my $key = $cols[0]." ".$cols[1]." ".$cols[2] ;
54 next if ( !defined $intronInfo{ $key } ) ;
55 my @infoCols = @{ $intronInfo{ $key } } ;
56 $infoCols[4] = $cols[4] if ( $infoCols[4] ne "+" || $infoCols[4] ne "-" ) ;
57 $infoCols[9] |= 2 ;
58
59 @{ $intronInfo{ $key } } = @infoCols ;
60 }
61 close FP1 ;
62
63 foreach my $key (sort sortIntron keys %intronInfo )
64 {
65 my @infoCols = @{ $intronInfo{ $key } } ;
66 #print join( " ", @infoCols ), "\n" ;
67
68 next if ( $infoCols[9] != 3 ) ;
69 pop @infoCols ;
70 print join( " ", @infoCols ), "\n" ;
71 }