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Revision 1.1 - (view) (download) (as text)
| 1 : | olson | 1.1 | # |
| 2 : | # Scan an NR, replacing the existing IDs with the corresponding principal | ||
| 3 : | # synonym id's from the given ID map file. | ||
| 4 : | # | ||
| 5 : | |||
| 6 : | use strict; | ||
| 7 : | |||
| 8 : | my $usage = "assign_synonym_ids_to_nr NR id.map NewNR"; | ||
| 9 : | |||
| 10 : | @ARGV == 3 or die $usage; | ||
| 11 : | |||
| 12 : | my $old_nr = shift; | ||
| 13 : | my $id_map = shift; | ||
| 14 : | my $new_nr = shift; | ||
| 15 : | |||
| 16 : | open(ONR, "<$old_nr") or die "Cannot open $old_nr for reading: $!\n"; | ||
| 17 : | open(MAP, "<$id_map") or die "Cannot open $id_map for reading: $!\n"; | ||
| 18 : | open(NNR, ">$new_nr") or die "Cannot open $new_nr for writing: $!\n"; | ||
| 19 : | |||
| 20 : | my %map; | ||
| 21 : | |||
| 22 : | while (<MAP>) | ||
| 23 : | { | ||
| 24 : | chomp; | ||
| 25 : | my($k,$v) = split(/\t/); | ||
| 26 : | $map{$k} = $v; | ||
| 27 : | } | ||
| 28 : | |||
| 29 : | close(MAP); | ||
| 30 : | |||
| 31 : | print "Read map\n"; | ||
| 32 : | |||
| 33 : | local $/ = "\n>"; | ||
| 34 : | |||
| 35 : | my($id, $rest, $seq); | ||
| 36 : | while (<ONR>) | ||
| 37 : | { | ||
| 38 : | chomp; | ||
| 39 : | if (($id, $rest, $seq) = /^>?(\S+)([^\n]*)\n(.*)/s) | ||
| 40 : | { | ||
| 41 : | my $new = $map{$id}; | ||
| 42 : | |||
| 43 : | if (!defined($new)) | ||
| 44 : | { | ||
| 45 : | warn "No mapped id found for $id\n"; | ||
| 46 : | $new = $id; | ||
| 47 : | } | ||
| 48 : | print NNR ">$new$rest\n$seq\n"; | ||
| 49 : | } | ||
| 50 : | } |
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