#609551805

Committed 11 Sep 2023 08:55AM UTC coverage: 83.134%. First build

Build # #609551805

Build Type

Pull #1039

travis-ci

Pull Request Pull Request #1039: Updating version to 112

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5.0

/modules/Bio/EnsEMBL/Variation/Pipeline/TranscriptFileAdaptor.pm

=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2025] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=cut


=head1 CONTACT

 Please email comments or questions to the public Ensembl
 developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

 Questions may also be sent to the Ensembl help desk at
 <http://www.ensembl.org/Help/Contact>.

=cut
package Bio::EnsEMBL::Variation::Pipeline::TranscriptFileAdaptor;

use strict;

use Digest::MD5 qw(md5_hex);

sub new {
    my $class = shift;

    my %args = @_;

    my $self = bless {}, $class;

    if ($args{fasta_file}) {
        $self->{fasta_file} = $args{fasta_file};
    }
    
    if ($args{transcripts}) {
        $self->_dump_translations($args{transcripts});
    }
    
    return $self;
}

sub get_translation_seq {
    my ($self, $translation_md5) = @_;

    my $fasta = $self->get_translation_fasta($translation_md5);

    $fasta =~ s/>.*\n//m;
    $fasta =~ s/\s//mg;

    return $fasta;
}

sub get_translation_fasta {
    my ($self, $translation_md5) = @_;
    
    my $file = $self->{fasta_file};
    
    my $fasta = `samtools faidx $file $translation_md5`;

    return $fasta;
}

sub get_all_translation_md5s {
    my $self = shift;

    my $fasta = $self->{fasta_file};

    my @ids = map {/>(.+)\n/; $1} `grep '>' $fasta`;

    return \@ids;
}

sub _dump_translations {

    my ($self, $transcripts) = @_;

    # dump the translations out to the FASTA file

    my $fasta = $self->{fasta_file};

    open my $FASTA, ">$fasta" or die "Failed to open $fasta for writing";

    # get rid of any existing index file

    if (-e "$fasta.fai") {
        unlink "$fasta.fai" or die "Failed to delete fasta index file";
    }

    my %seen_md5;

    for my $transcript (@$transcripts) {

        my $tl = $transcript->translation;
    
        next unless $tl;

        my $protein = $tl->seq;

        my $md5 = md5_hex($protein);

        next if $seen_md5{$md5}++;

        $protein =~ s/(.{80})/$1\n/g;

        # get rid of any trailing newline
        chomp $protein;

        print $FASTA ">$md5\n$protein\n";
    }

    close $FASTA;

    # index the file

    `samtools faidx $fasta`;
}
 

1;

1	=head1 LICENSE
2
3	Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
4	Copyright [2016-2025] EMBL-European Bioinformatics Institute
5
6	Licensed under the Apache License, Version 2.0 (the "License");
7	you may not use this file except in compliance with the License.
8	You may obtain a copy of the License at
9
10	http://www.apache.org/licenses/LICENSE-2.0
11
12	Unless required by applicable law or agreed to in writing, software
13	distributed under the License is distributed on an "AS IS" BASIS,
14	WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15	See the License for the specific language governing permissions and
16	limitations under the License.
17
18	=cut
19
20
21	=head1 CONTACT
22
23	Please email comments or questions to the public Ensembl
24	developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
25
26	Questions may also be sent to the Ensembl help desk at
27	<http://www.ensembl.org/Help/Contact>.
28
29	=cut
30	package Bio::EnsEMBL::Variation::Pipeline::TranscriptFileAdaptor;
31
32	use strict;	1✔
33
34	use Digest::MD5 qw(md5_hex);	1✔
35
36	sub new {
37	my $class = shift;	×
38
39	my %args = @_;	×
40
41	my $self = bless {}, $class;	×
42
43	if ($args{fasta_file}) {	×
44	$self->{fasta_file} = $args{fasta_file};	×
45	}
46
47	if ($args{transcripts}) {	×
48	$self->_dump_translations($args{transcripts});	×
49	}
50
51	return $self;	×
52	}
53
54	sub get_translation_seq {
55	my ($self, $translation_md5) = @_;	×
56
57	my $fasta = $self->get_translation_fasta($translation_md5);	×
58
59	$fasta =~ s/>.*\n//m;	×
60	$fasta =~ s/\s//mg;	×
61
62	return $fasta;	×
63	}
64
65	sub get_translation_fasta {
66	my ($self, $translation_md5) = @_;	×
67
68	my $file = $self->{fasta_file};	×
69
70	my $fasta = `samtools faidx $file $translation_md5`;	×
71
72	return $fasta;	×
73	}
74
75	sub get_all_translation_md5s {
76	my $self = shift;	×
77
78	my $fasta = $self->{fasta_file};	×
79
80	my @ids = map {/>(.+)\n/; $1} `grep '>' $fasta`;	×
81
82	return \@ids;	×
83	}
84
85	sub _dump_translations {
86
87	my ($self, $transcripts) = @_;	×
88
89	# dump the translations out to the FASTA file
90
91	my $fasta = $self->{fasta_file};	×
92
93	open my $FASTA, ">$fasta" or die "Failed to open $fasta for writing";	×
94
95	# get rid of any existing index file
96
97	if (-e "$fasta.fai") {	×
98	unlink "$fasta.fai" or die "Failed to delete fasta index file";	×
99	}
100
101	my %seen_md5;	×
102
103	for my $transcript (@$transcripts) {	×
104
105	my $tl = $transcript->translation;	×
106
107	next unless $tl;	×
108
109	my $protein = $tl->seq;	×
110
111	my $md5 = md5_hex($protein);	×
112
113	next if $seen_md5{$md5}++;	×
114
115	$protein =~ s/(.{80})/$1\n/g;	×
116
117	# get rid of any trailing newline
118	chomp $protein;	×
119
120	print $FASTA ">$md5\n$protein\n";	×
121	}
122
123	close $FASTA;	×
124
125	# index the file
126
127	`samtools faidx $fasta`;	×
128	}
129
130
131	1;

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