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Revision 1.4 - (view) (download) (as text)
| 1 : | olson | 1.4 | # |
| 2 : | # Copyright (c) 2003-2006 University of Chicago and Fellowship | ||
| 3 : | # for Interpretations of Genomes. All Rights Reserved. | ||
| 4 : | # | ||
| 5 : | # This file is part of the SEED Toolkit. | ||
| 6 : | # | ||
| 7 : | # The SEED Toolkit is free software. You can redistribute | ||
| 8 : | # it and/or modify it under the terms of the SEED Toolkit | ||
| 9 : | # Public License. | ||
| 10 : | # | ||
| 11 : | # You should have received a copy of the SEED Toolkit Public License | ||
| 12 : | # along with this program; if not write to the University of Chicago | ||
| 13 : | # at info@ci.uchicago.edu or the Fellowship for Interpretation of | ||
| 14 : | # Genomes at veronika@thefig.info or download a copy from | ||
| 15 : | # http://www.theseed.org/LICENSE.TXT. | ||
| 16 : | # | ||
| 17 : | |||
| 18 : | overbeek | 1.1 | |
| 19 : | $usage = "match_dna_to_aligned_prots dna_filename aligned_prot_filename"; | ||
| 20 : | |||
| 21 : | (($dna_filename = shift @ARGV) && ($aligned_prot_filename = shift @ARGV)) || | ||
| 22 : | die $usage; | ||
| 23 : | |||
| 24 : | open(DNA,"<$dna_filename") or die "failed to open dna"; | ||
| 25 : | open(PROT,"<$aligned_prot_filename") or die "failed to open prot"; | ||
| 26 : | while (defined($line = <DNA>)) | ||
| 27 : | { | ||
| 28 : | $line =~ />(\S+)/; | ||
| 29 : | $id = $1; | ||
| 30 : | $seq = <DNA>; | ||
| 31 : | chomp $seq; | ||
| 32 : | $dnaseqs{$id} = $seq; | ||
| 33 : | } | ||
| 34 : | |||
| 35 : | while (defined($line = <PROT>)) | ||
| 36 : | { | ||
| 37 : | $line =~ />(\S+)/; | ||
| 38 : | $id = $1; | ||
| 39 : | $seq = <PROT>; | ||
| 40 : | chomp $seq; | ||
| 41 : | $protseqs{$id} = $seq; | ||
| 42 : | } | ||
| 43 : | |||
| 44 : | # for $id (keys(%protseqs)) { print "$id $protseqs{$id}\n"; } | ||
| 45 : | # for $id (keys(%protseqs)) { print "$id $protseqs{$id}\n" if ($id =~ /1048/); } | ||
| 46 : | ## for $id (keys(%protseqs)) | ||
| 47 : | ## { | ||
| 48 : | ## $protseqs{$id} =~ /(\-+)/; | ||
| 49 : | ## $subseq=$1; | ||
| 50 : | ## # print "$id NUM ", length($subseq), $subseq, "\n" if ($id =~ /155920.*1503/); | ||
| 51 : | ## print "$id NUM=", length($subseq), "\n"; | ||
| 52 : | ## } | ||
| 53 : | |||
| 54 : | for $id (keys(%protseqs)) | ||
| 55 : | { | ||
| 56 : | $protseq = $protseqs{$id}; | ||
| 57 : | @protseq = split('',$protseq); | ||
| 58 : | $newprotseq = ''; | ||
| 59 : | for ($i=0; $i < @protseq; $i++) | ||
| 60 : | { | ||
| 61 : | $newprotseq .= "$protseq[$i] "; | ||
| 62 : | } | ||
| 63 : | @newprotseq = split('',$newprotseq); | ||
| 64 : | $protseqs{$id} = $newprotseq; | ||
| 65 : | # print "$id $newprotseq\n" if ($id =~ /1048/); | ||
| 66 : | $dnaseq = $dnaseqs{$id}; | ||
| 67 : | $dnaidx = 0; | ||
| 68 : | $newdnaseq = ''; | ||
| 69 : | for ($i=0; $i < @protseq; $i++) | ||
| 70 : | { | ||
| 71 : | $c = $protseq[$i]; | ||
| 72 : | if ($c =~ /[A-Z]/) | ||
| 73 : | { | ||
| 74 : | $newdnaseq .= substr($dnaseq,$dnaidx,3); | ||
| 75 : | $dnaidx += 3; | ||
| 76 : | } | ||
| 77 : | elsif ($c eq '-') | ||
| 78 : | { | ||
| 79 : | $newdnaseq .= "---"; | ||
| 80 : | } | ||
| 81 : | else | ||
| 82 : | { | ||
| 83 : | print STDERR "unrecognized char $c\n"; | ||
| 84 : | } | ||
| 85 : | } | ||
| 86 : | $dnaseqs{$id} = $newdnaseq; | ||
| 87 : | # print "$id $newdnaseq\n" if ($id =~ /1048/); | ||
| 88 : | # sanity check | ||
| 89 : | if (length($newdnaseq) != length($newprotseq)) | ||
| 90 : | { | ||
| 91 : | print STDERR "BAD LEN $id ", length($newdnaseq), " ", length($newprotseq), "\n"; | ||
| 92 : | } | ||
| 93 : | overbeek | 1.3 | $dnaid = "DNA_" . $id; |
| 94 : | $proid = "PRO_" . $id; | ||
| 95 : | overbeek | 1.1 | print ">$dnaid\n$newdnaseq\n"; |
| 96 : | print ">$proid\n$newprotseq\n"; | ||
| 97 : | } |
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