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comparison 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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0:54c7a3ea81e2 1:8691c1c61a8e
1 package CPT::External::LipoP;
2 no warnings;
3 use Moose;
4 use File::Temp qw(tempfile);
5 use IPC::Run qw(run);
6
7 has 'sequence' => ( is => 'rw', isa => 'Str' );
8 has 'response' => ( is => 'rw', isa => 'Str' );
9 has 'cleavage' => ( is => 'rw', isa => 'ArrayRef' );
10 has 'tmpfile' => (is => 'rw', isa => 'Any');
11
12 sub create_fasta_file {
13 my ( $self, $seq ) = @_;
14 my ( $fh, $filename ) = tempfile( "cpt.lipop.XXXXXXX", UNLINK => 1 );
15
16 #printf $fh ">%s\n%s\n", 'seq', $seq;
17 printf $fh "%s\n", $seq;
18 close($fh);
19 return $filename;
20 }
21
22 sub parse_text {
23 my ($self) = @_;
24
25 foreach my $line ( split( /\n/, $self->response() ) ) {
26 if ( $line =~ /#.*cleavage=(\d+)-(\d+)/ ) {
27 $self->cleavage( [ $1, $2 ] );
28 }
29 }
30 # # seq SpII score=17.8897 margin=13.48964 cleavage=19-20 Pos+2=K
31 # # Cut-off=-3
32 # seq LipoP1.0:Best SpII 1 1 17.8897
33 # seq LipoP1.0:Margin SpII 1 1 13.48964
34 # seq LipoP1.0:Class SpI 1 1 4.40006
35 # seq LipoP1.0:Class CYT 1 1 -0.200913
36 # seq LipoP1.0:Signal CleavII 19 20 17.8897 # LVVSA|CKSPP Pos+2=K
37 # seq LipoP1.0:Signal CleavI 28 29 4.03409 # PPVQS|QRPEP
38 # seq LipoP1.0:Signal CleavI 21 22 2.04071 # VSACK|SPPPV
39 # seq LipoP1.0:Signal CleavI 27 28 -2.07502 # PPPVQ|SQRPE
40 # seq LipoP1.0:Signal CleavI 19 20 -2.6907 # LVVSA|CKSPP
41 # seq LipoP1.0:Signal CleavI 22 23 -2.87659 # SACKS|PPPVQ
42 }
43
44 sub analyze {
45 my ( $self, $seq ) = @_;
46 $self->sequence($seq);
47 $self->tmpfile($self->create_fasta_file($seq));
48 my @cmd = ( 'LipoP', $self->tmpfile(), '-workdir', '/tmp/nonexistant/', '-wwwdir', '/tmp/nonexistant' );
49 my ( $in, $out, $err );
50 run \@cmd, \$in, \$out, \$err;
51 if ($err) { print "Error: $err\n"; }
52 $self->response($out);
53 $self->parse_text();
54 unlink($self->tmpfile());
55 }
56
57 sub cleanup {
58 my ($self) = @_;
59 return;
60 }
61
62
63 no Moose;
64 1;
65
66 __END__
67
68 =pod
69
70 =encoding UTF-8
71
72 =head1 NAME
73
74 CPT::External::LipoP
75
76 =head1 VERSION
77
78 version 1.99.4
79
80 =head1 AUTHOR
81
82 Eric Rasche <rasche.eric@yandex.ru>
83
84 =head1 COPYRIGHT AND LICENSE
85
86 This software is Copyright (c) 2014 by Eric Rasche.
87
88 This is free software, licensed under:
89
90 The GNU General Public License, Version 3, June 2007
91
92 =cut