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annotate lib/CPT/External/LipoP.pm @ 1:8691c1c61a8e draft default tip

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:48:47 +0000
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1 package CPT::External::LipoP;
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2 no warnings;
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3 use Moose;
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4 use File::Temp qw(tempfile);
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5 use IPC::Run qw(run);
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6
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7 has 'sequence' => ( is => 'rw', isa => 'Str' );
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8 has 'response' => ( is => 'rw', isa => 'Str' );
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9 has 'cleavage' => ( is => 'rw', isa => 'ArrayRef' );
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10 has 'tmpfile' => (is => 'rw', isa => 'Any');
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11
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12 sub create_fasta_file {
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13 my ( $self, $seq ) = @_;
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14 my ( $fh, $filename ) = tempfile( "cpt.lipop.XXXXXXX", UNLINK => 1 );
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15
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16 #printf $fh ">%s\n%s\n", 'seq', $seq;
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17 printf $fh "%s\n", $seq;
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18 close($fh);
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19 return $filename;
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20 }
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21
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22 sub parse_text {
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23 my ($self) = @_;
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24
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25 foreach my $line ( split( /\n/, $self->response() ) ) {
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26 if ( $line =~ /#.*cleavage=(\d+)-(\d+)/ ) {
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27 $self->cleavage( [ $1, $2 ] );
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28 }
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29 }
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30 # # seq SpII score=17.8897 margin=13.48964 cleavage=19-20 Pos+2=K
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31 # # Cut-off=-3
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32 # seq LipoP1.0:Best SpII 1 1 17.8897
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33 # seq LipoP1.0:Margin SpII 1 1 13.48964
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34 # seq LipoP1.0:Class SpI 1 1 4.40006
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35 # seq LipoP1.0:Class CYT 1 1 -0.200913
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36 # seq LipoP1.0:Signal CleavII 19 20 17.8897 # LVVSA|CKSPP Pos+2=K
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37 # seq LipoP1.0:Signal CleavI 28 29 4.03409 # PPVQS|QRPEP
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38 # seq LipoP1.0:Signal CleavI 21 22 2.04071 # VSACK|SPPPV
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39 # seq LipoP1.0:Signal CleavI 27 28 -2.07502 # PPPVQ|SQRPE
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40 # seq LipoP1.0:Signal CleavI 19 20 -2.6907 # LVVSA|CKSPP
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41 # seq LipoP1.0:Signal CleavI 22 23 -2.87659 # SACKS|PPPVQ
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42 }
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43
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44 sub analyze {
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45 my ( $self, $seq ) = @_;
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46 $self->sequence($seq);
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47 $self->tmpfile($self->create_fasta_file($seq));
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48 my @cmd = ( 'LipoP', $self->tmpfile(), '-workdir', '/tmp/nonexistant/', '-wwwdir', '/tmp/nonexistant' );
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49 my ( $in, $out, $err );
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50 run \@cmd, \$in, \$out, \$err;
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51 if ($err) { print "Error: $err\n"; }
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52 $self->response($out);
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53 $self->parse_text();
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54 unlink($self->tmpfile());
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55 }
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56
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57 sub cleanup {
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58 my ($self) = @_;
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59 return;
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60 }
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61
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62
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63 no Moose;
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64 1;
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65
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66 __END__
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67
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68 =pod
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69
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70 =encoding UTF-8
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71
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72 =head1 NAME
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73
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74 CPT::External::LipoP
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75
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76 =head1 VERSION
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77
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78 version 1.99.4
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79
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80 =head1 AUTHOR
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81
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82 Eric Rasche <rasche.eric@yandex.ru>
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83
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84 =head1 COPYRIGHT AND LICENSE
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85
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86 This software is Copyright (c) 2014 by Eric Rasche.
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87
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88 This is free software, licensed under:
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89
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90 The GNU General Public License, Version 3, June 2007
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91
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92 =cut