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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:50:07 +0000
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1 package CPT::External::TMHMM;
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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 use File::Temp qw(tempdir);
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7 use File::Copy qw(move);
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8
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9 has 'sequence' => ( is => 'rw', isa => 'Str' );
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10 has 'response' => ( is => 'rw', isa => 'Str' );
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11
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12 has 'num_predicted' => ( is => 'rw', isa => 'Int' );
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13 has 'predicted_locations' => ( is => 'rw', isa => 'ArrayRef' );
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14 has 'prob_n_in' => ( is => 'rw', isa => 'Str' );
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15 has 'hash' => ( is => 'rw', isa => 'Str' );
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16 has 'picture_location' => ( is => 'rw', isa => 'Str' );
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17
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18 my ( $fh, $filename, $image );
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19
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20 sub create_fasta_file {
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21 my ( $self, $seq ) = @_;
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22 ( $fh, $filename ) = tempfile( "cpt.tmhmm.XXXXXXX", UNLINK => 1 );
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23
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24 #printf $fh ">%s\n%s\n", 'seq', $seq;
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25 printf $fh "%s\n", $seq;
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26 return $filename;
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27 }
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28
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29 sub parse_text {
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30 my ($self) = @_;
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31 unless ( $self->predicted_locations() ) {
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32 $self->predicted_locations( [] );
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33 }
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34 unless ( $self->num_predicted() ) {
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35 $self->num_predicted(0);
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36 }
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37 foreach my $line ( split( /\n/, $self->response() ) ) {
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38 if ( $line =~ /Number of predicted TMHs:\s*(\d+)/ ) {
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39 $self->num_predicted($1);
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40 }
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41 elsif ( $line =~ /Total prob of N-in:\s*([0-9.]*)/ ) {
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42 $self->prob_n_in($1);
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43 }
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44 elsif ( $line =~ /TMHMM2.0\s*TMhelix\s*([0-9]+)\s*([0-9]+)/ ) {
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45
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46 #$self->num_predicted($self->num_predicted()+1);
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47 push( @{ $self->predicted_locations() }, [ $1, $2 ] );
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48 }
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49 }
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50
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51 # # seq Length: 145
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52 # # seq Number of predicted TMHs: 1
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53 # # seq Exp number of AAs in TMHs: 20.91302
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54 # # seq Exp number, first 60 AAs: 20.91265
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55 # # seq Total prob of N-in: 0.04659
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56 # # seq POSSIBLE N-term signal sequence
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57 # seq TMHMM2.0 outside 1 3
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58 # seq TMHMM2.0 TMhelix 4 23
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59 # seq TMHMM2.0 inside 24 145
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60 }
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61
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62 sub analyze {
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63 my ( $self, $seq ) = @_;
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64
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65 # Set our hash
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66 require Digest::MD5;
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67 $self->hash( Digest::MD5::md5_hex($seq) );
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68
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69 # Set our sequence
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70 $self->sequence($seq);
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71
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72 # Tmp dir to run in
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73 my $dir = tempdir( CLEANUP => 1 );
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74 my $tmpfile = $self->create_fasta_file($seq);
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75
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76 # Plot and use specified workdir
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77 my @cmd = ( 'tmhmm.pl', '-plot', '-workdir', $dir, '<', $tmpfile );
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78
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79 # Run the command
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80 my ( $in, $out, $err );
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81 run \@cmd, \$in, \$out, \$err;
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82
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83 # If error,we error
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84 if ($err) {
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85
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86 # print STDERR "Error: $err\n";
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87 # Kinda a crappy way to handle this...
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88 $self->response($err);
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89 return 0;
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90 }
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91 {
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92
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93 # Move the created plot to a known location
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94 my @tmhmm_files = glob("$dir/*/*.png");
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95
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96 # There's really only one png but this is just as easy to write
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97 for my $png (@tmhmm_files) {
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98 $image = sprintf( "/tmp/cpt.ext.tmhmm.%s.png", $self->hash() );
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99 move( $png, $image );
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100 }
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101
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102 # Module to remove the temporary dir so we clean up after
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103 # ourselves quickly, since this programme seems to open a LARGE
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104 # number of file handles.
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105 require File::Path;
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106 File::Path::remove_tree($dir);
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107
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108 # set response and parse it, then return OK.
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109 $self->response($out);
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110 $self->parse_text();
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111 return 1;
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112 }
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113 }
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114
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115 sub cleanup {
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116 if ( defined($fh) ) {
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117 close($fh);
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118 unlink($filename);
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119 if ( -e $image ) {
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120 unlink($image);
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121 }
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122 }
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123 }
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124
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125 END {
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126 if ( defined($fh) ) {
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127 close($fh);
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128 unlink($filename);
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129 if ( -e $image ) {
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130 unlink($image);
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131 }
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132 }
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133 }
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134
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135 no Moose;
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136 1;
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137
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138 __END__
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139
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140 =pod
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141
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142 =encoding UTF-8
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143
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144 =head1 NAME
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145
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146 CPT::External::TMHMM
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147
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148 =head1 VERSION
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149
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150 version 1.99.4
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151
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152 =head1 AUTHOR
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153
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154 Eric Rasche <rasche.eric@yandex.ru>
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155
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156 =head1 COPYRIGHT AND LICENSE
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157
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158 This software is Copyright (c) 2014 by Eric Rasche.
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159
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160 This is free software, licensed under:
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161
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162 The GNU General Public License, Version 3, June 2007
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163
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164 =cut