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Revision 1.2 - (view) (download) (as text)
| 1 : | olson | 1.2 | # |
| 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 | # usage: ali_to_seq < ali > seqs |
| 19 : | |||
| 20 : | $/ = "\n>"; | ||
| 21 : | while (defined($_ = <STDIN>)) | ||
| 22 : | { | ||
| 23 : | chomp; | ||
| 24 : | if ($_ =~ /^>?(\S+)[^\n]*\n(.*)/s) | ||
| 25 : | { | ||
| 26 : | $id = $1; | ||
| 27 : | $seq = $2; | ||
| 28 : | $seq =~ s/\n//gs; | ||
| 29 : | $seq =~ s/ //gs; | ||
| 30 : | $seq =~ s/[\-\.\~]//gs; | ||
| 31 : | $seq = lc $seq; | ||
| 32 : | $seq =~ s/u/t/g; | ||
| 33 : | &display_id_and_seq($id,\$seq); | ||
| 34 : | } | ||
| 35 : | } | ||
| 36 : | |||
| 37 : | sub display_id_and_seq { | ||
| 38 : | my( $id, $seq, $fh ) = @_; | ||
| 39 : | |||
| 40 : | if (! defined($fh) ) { $fh = \*STDOUT; } | ||
| 41 : | |||
| 42 : | print $fh ">$id\n"; | ||
| 43 : | &display_seq($seq, $fh); | ||
| 44 : | } | ||
| 45 : | |||
| 46 : | sub display_seq { | ||
| 47 : | my ( $seq, $fh ) = @_; | ||
| 48 : | my ( $i, $n, $ln ); | ||
| 49 : | |||
| 50 : | if (! defined($fh) ) { $fh = \*STDOUT; } | ||
| 51 : | |||
| 52 : | $n = length($$seq); | ||
| 53 : | # confess "zero-length sequence ???" if ( (! defined($n)) || ($n == 0) ); | ||
| 54 : | for ($i=0; ($i < $n); $i += 60) | ||
| 55 : | { | ||
| 56 : | if (($i + 60) <= $n) | ||
| 57 : | { | ||
| 58 : | $ln = substr($$seq,$i,60); | ||
| 59 : | } | ||
| 60 : | else | ||
| 61 : | { | ||
| 62 : | $ln = substr($$seq,$i,($n-$i)); | ||
| 63 : | } | ||
| 64 : | print $fh "$ln\n"; | ||
| 65 : | } | ||
| 66 : | } |
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