f92b9ad53

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<a href="https://github.com/Clinical-Genomics/MIP/commit/<a class=hub.com/Clinical-Genomics/MIP/commit/f92b9ad5348c9429c0dd2b5db6e68f955a3b6b01">f92b9ad53<a href="https://github.com/Clinical-Genomics/MIP/commit/f92b9ad5348c9429c0dd2b5db6e68f955a3b6b01">">Merge </a><a class="double-link" href="https://github.com/Clinical-Genomics/MIP/commit/<a class="double-link" href="https://github.com/Clinical-Genomics/MIP/commit/908b6c8a5598aa1beaf44b07af8d1f5f6d261df9">908b6c8a5</a>">908b6c8a5</a><a href="https://github.com/Clinical-Genomics/MIP/commit/f92b9ad5348c9429c0dd2b5db6e68f955a3b6b01"> into 3a7904127">3a7904127</a>

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98.11

/lib/MIP/Program/Stringtie.pm

package MIP::Program::Stringtie;

use 5.026;
use Carp;
use charnames qw{ :full :short };
use English qw{ -no_match_vars };
use open qw{ :encoding(UTF-8) :std };
use Params::Check qw{ allow check last_error };
use utf8;
use warnings;
use warnings qw{ FATAL utf8 };

## CPANM
use autodie qw{ :all };
use Readonly;

## MIPs lib/
use MIP::Constants qw{ $SPACE };
use MIP::Environment::Executable qw{ get_executable_base_command };
use MIP::Unix::Standard_streams qw{ unix_standard_streams };
use MIP::Unix::Write_to_file qw{ unix_write_to_file };

BEGIN {
    require Exporter;
    use base qw{ Exporter };

    # Functions and variables which can be optionally exported
    our @EXPORT_OK = qw{ stringtie };
}

sub stringtie {

## Function : Perl wrapper for StringTie. Based on version 1.3.4.
## Returns  : @commands
## Arguments: $cov_ref_transcripts_outfile_path => Fully covered reference transcripts
##          : $filehandle                       => Filehandle to write to
##          : $gene_abundance_outfile_path      => Gene aboundances
##          : $gtf_reference_path               => Input GTF refrence file
##          : $infile_path                      => Input bam file path
##          : $junction_reads                   => Required number of junction spanning reads
##          : $library_type                     => Orientation and strandedness of the library
##          : $minimum_coverage                 => Only output transcripts with coverage above this value
##          : $outfile_path                     => Path to output GTF
##          : $stderrfile_path                  => Stderrfile path
##          : $stderrfile_path_append           => Append stderr info to file path
##          : $stdoutfile_path                  => Stdoutfile path
##          : $threads                          => Number of threads

    my ($arg_href) = @_;

    ## Flatten argument(s)
    my $cov_ref_transcripts_outfile_path;
    my $filehandle;
    my $gene_abundance_outfile_path;
    my $gtf_reference_path;
    my $infile_path;
    my $junction_reads;
    my $library_type;
    my $minimum_coverage;
    my $outfile_path;
    my $stderrfile_path;
    my $stderrfile_path_append;
    my $stdoutfile_path;
    my $threads;

    my $tmpl = {
        cov_ref_transcripts_outfile_path => {
            store       => \$cov_ref_transcripts_outfile_path,
            strict_type => 1,
        },
        filehandle => {
            store => \$filehandle,
        },
        gene_abundance_outfile_path => {
            store       => \$gene_abundance_outfile_path,
            strict_type => 1,
        },
        gtf_reference_path => {
            defined     => 1,
            required    => 1,
            store       => \$gtf_reference_path,
            strict_type => 1,
        },
        infile_path => {
            defined     => 1,
            required    => 1,
            store       => \$infile_path,
            strict_type => 1,
        },
        junction_reads => {
            store       => \$junction_reads,
            strict_type => 1,
        },
        library_type => {
            defined     => 1,
            store       => \$library_type,
            strict_type => 1,
        },
        minimum_coverage => {
            store       => \$minimum_coverage,
            strict_type => 1,
        },
        outfile_path => {
            defined     => 1,
            required    => 1,
            store       => \$outfile_path,
            strict_type => 1,
        },
        stderrfile_path => {
            store       => \$stderrfile_path,
            strict_type => 1,
        },
        stderrfile_path_append => {
            store       => \$stderrfile_path_append,
            strict_type => 1,
        },
        stdoutfile_path => {
            store       => \$stdoutfile_path,
            strict_type => 1,
        },
        threads => {
            store       => \$threads,
            strict_type => 1,
        },
    };

    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};

    my @commands = ( get_executable_base_command( { base_command => q{stringtie}, } ), );

    push @commands, $infile_path;

    if ($cov_ref_transcripts_outfile_path) {
        push @commands, q{-C} . $SPACE . $cov_ref_transcripts_outfile_path;
    }

    if ($gene_abundance_outfile_path) {
        push @commands, q{-A} . $SPACE . $gene_abundance_outfile_path;
    }

    push @commands, q{-G} . $SPACE . $gtf_reference_path;

    if ($junction_reads) {
        push @commands, q{-j} . $SPACE . $junction_reads;
    }

    if ( $library_type and $library_type eq q{forward_stranded} ) {
        push @commands, q{--fr};
    }
    elsif ( $library_type and $library_type eq q{reverse_stranded} ) {
        push @commands, q{--rf};
    }

    if ($minimum_coverage) {
        push @commands, q{-c} . $SPACE . $minimum_coverage;
    }

    if ($threads) {
        push @commands, q{-p} . $SPACE . $threads;
    }

    push @commands, q{-o} . $SPACE . $outfile_path;

    push @commands,
      unix_standard_streams(
        {
            stderrfile_path        => $stderrfile_path,
            stderrfile_path_append => $stderrfile_path_append,
            stdoutfile_path        => $stdoutfile_path,
        }
      );

    unix_write_to_file(
        {
            commands_ref => \@commands,
            filehandle   => $filehandle,
            separator    => $SPACE,

        }
    );
    return @commands;
}

1;

1	package MIP::Program::Stringtie;
2
3	use 5.026;	17✔
4	use Carp;	17✔
5	use charnames qw{ :full :short };	17✔
6	use English qw{ -no_match_vars };	17✔
7	use open qw{ :encoding(UTF-8) :std };	17✔
8	use Params::Check qw{ allow check last_error };	17✔
9	use utf8;	17✔
10	use warnings;	17✔
11	use warnings qw{ FATAL utf8 };	17✔
12
13	## CPANM
14	use autodie qw{ :all };	17✔
15	use Readonly;	17✔
16
17	## MIPs lib/
18	use MIP::Constants qw{ $SPACE };	17✔
19	use MIP::Environment::Executable qw{ get_executable_base_command };	17✔
20	use MIP::Unix::Standard_streams qw{ unix_standard_streams };	17✔
21	use MIP::Unix::Write_to_file qw{ unix_write_to_file };	17✔
22
23	BEGIN {
24	require Exporter;	17✔
25	use base qw{ Exporter };	17✔
26
27	# Functions and variables which can be optionally exported
28	our @EXPORT_OK = qw{ stringtie };	17✔
29	}
30
31	sub stringtie {
32
33	## Function : Perl wrapper for StringTie. Based on version 1.3.4.
34	## Returns : @commands
35	## Arguments: $cov_ref_transcripts_outfile_path => Fully covered reference transcripts
36	## : $filehandle => Filehandle to write to
37	## : $gene_abundance_outfile_path => Gene aboundances
38	## : $gtf_reference_path => Input GTF refrence file
39	## : $infile_path => Input bam file path
40	## : $junction_reads => Required number of junction spanning reads
41	## : $library_type => Orientation and strandedness of the library
42	## : $minimum_coverage => Only output transcripts with coverage above this value
43	## : $outfile_path => Path to output GTF
44	## : $stderrfile_path => Stderrfile path
45	## : $stderrfile_path_append => Append stderr info to file path
46	## : $stdoutfile_path => Stdoutfile path
47	## : $threads => Number of threads
48
49	my ($arg_href) = @_;	14✔
50
51	## Flatten argument(s)
52	my $cov_ref_transcripts_outfile_path;	14✔
53	my $filehandle;
54	my $gene_abundance_outfile_path;	14✔
55	my $gtf_reference_path;	14✔
56	my $infile_path;	14✔
57	my $junction_reads;	14✔
58	my $library_type;	14✔
59	my $minimum_coverage;	14✔
60	my $outfile_path;	14✔
61	my $stderrfile_path;	14✔
62	my $stderrfile_path_append;	14✔
63	my $stdoutfile_path;	14✔
64	my $threads;	14✔
65
66	my $tmpl = {	14✔
67	cov_ref_transcripts_outfile_path => {
68	store => \$cov_ref_transcripts_outfile_path,
69	strict_type => 1,
70	},
71	filehandle => {
72	store => \$filehandle,
73	},
74	gene_abundance_outfile_path => {
75	store => \$gene_abundance_outfile_path,
76	strict_type => 1,
77	},
78	gtf_reference_path => {
79	defined => 1,
80	required => 1,
81	store => \$gtf_reference_path,
82	strict_type => 1,
83	},
84	infile_path => {
85	defined => 1,
86	required => 1,
87	store => \$infile_path,
88	strict_type => 1,
89	},
90	junction_reads => {
91	store => \$junction_reads,
92	strict_type => 1,
93	},
94	library_type => {
95	defined => 1,
96	store => \$library_type,
97	strict_type => 1,
98	},
99	minimum_coverage => {
100	store => \$minimum_coverage,
101	strict_type => 1,
102	},
103	outfile_path => {
104	defined => 1,
105	required => 1,
106	store => \$outfile_path,
107	strict_type => 1,
108	},
109	stderrfile_path => {
110	store => \$stderrfile_path,
111	strict_type => 1,
112	},
113	stderrfile_path_append => {
114	store => \$stderrfile_path_append,
115	strict_type => 1,
116	},
117	stdoutfile_path => {
118	store => \$stdoutfile_path,
119	strict_type => 1,
120	},
121	threads => {
122	store => \$threads,
123	strict_type => 1,
124	},
125	};
126
127	check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};	14✔
128
129	my @commands = ( get_executable_base_command( { base_command => q{stringtie}, } ), );	14✔
130
131	push @commands, $infile_path;	14✔
132
133	if ($cov_ref_transcripts_outfile_path) {	14✔
134	push @commands, q{-C} . $SPACE . $cov_ref_transcripts_outfile_path;	2✔
135	}
136
137	if ($gene_abundance_outfile_path) {	14✔
138	push @commands, q{-A} . $SPACE . $gene_abundance_outfile_path;	2✔
139	}
140
141	push @commands, q{-G} . $SPACE . $gtf_reference_path;	14✔
142
143	if ($junction_reads) {	14✔
144	push @commands, q{-j} . $SPACE . $junction_reads;	1✔
145	}
146
147	if ( $library_type and $library_type eq q{forward_stranded} ) {	14✔
148	push @commands, q{--fr};	1✔
149	}
150	elsif ( $library_type and $library_type eq q{reverse_stranded} ) {
151	push @commands, q{--rf};	×
152	}
153
154	if ($minimum_coverage) {	14✔
155	push @commands, q{-c} . $SPACE . $minimum_coverage;	1✔
156	}
157
158	if ($threads) {	14✔
159	push @commands, q{-p} . $SPACE . $threads;	2✔
160	}
161
162	push @commands, q{-o} . $SPACE . $outfile_path;	14✔
163
164	push @commands,	14✔
165	unix_standard_streams(
166	{
167	stderrfile_path => $stderrfile_path,
168	stderrfile_path_append => $stderrfile_path_append,
169	stdoutfile_path => $stdoutfile_path,
170	}
171	);
172
173	unix_write_to_file(	14✔
174	{
175	commands_ref => \@commands,
176	filehandle => $filehandle,
177	separator => $SPACE,
178
179	}
180	);
181	return @commands;	14✔
182	}
183
184	1;

Clinical-Genomics / MIP / f92b9ad53

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