Mercurial > repos > cpt > cpt_psm_recombine

annotate lib/CPT/Bio/SAR.pm @ 1:97ef96676b48 draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:51:26 +0000
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1 package CPT::Bio::SAR;
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2 use strict;
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3 use warnings;
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4 use autodie;
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5 use Moose;
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6
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7 sub filter_sar {
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8 my ($self, @seqs) = @_;
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9 my @good;
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10 foreach(@seqs){
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11 if(has_sar_motif($_)){
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12 push(@good, $_);
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13 }
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14 }
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15 return @good;
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16 }
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17
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18 sub has_sar_motif {
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19 my ( $self, $seq ) = @_;
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20
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21 return 0 if(length $seq < 40);
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22
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23 my $reg_a = qr/([^DEKR]{3}K[^DEKR]{8,}[^DER]{1}[^DEKR]{3})/;
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24 my $reg_b = qr/([KR]{1,}[^DEKR]{12,}[^DER]{1}[^DEKR]{3})/;
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25
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26 my $first40 = substr( $seq, 0, 40 );
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27
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28 # there is a transmembrane domain in the first 40 AAs
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29 # there is at least one positive charged AAs in front of the TMD
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30 if ( $first40 =~ $reg_a || $first40 =~ $reg_b ) {
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31 my $modi1st40 = $first40;
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32 # Cut out the match, and then add the whole thing to the end.
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33 my $t4homology =
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34 #substr($seq,0, $-[0] ), # Before the match
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35 #substr($seq, $-[0], ($+[0] - $-[0])), # the match
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36 substr($seq, $+[0]). # After the match
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37 $first40;
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38 $t4homology = substr($t4homology, 0 , 40);
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39
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40 if ( $t4homology =~ qr/E[A-Z]{8}[DC][A-Z]{4,5}T/ ) {
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41 return 1;
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42 }
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43 }
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44 return 0;
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45 }
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46
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47 no Moose;
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48 1;
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49
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50 __END__
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51
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52 =pod
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53
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54 =encoding UTF-8
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55
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56 =head1 NAME
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57
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58 CPT::Bio::SAR
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59
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60 =head1 VERSION
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61
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62 version 1.99.4
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63
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64 =head1 AUTHOR
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65
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66 Eric Rasche <rasche.eric@yandex.ru>
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67
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68 =head1 COPYRIGHT AND LICENSE
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69
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70 This software is Copyright (c) 2014 by Eric Rasche.
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71
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72 This is free software, licensed under:
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73
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74 The GNU General Public License, Version 3, June 2007
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75
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76 =cut