/usr/share/perl5/Bio/Tools/Run/Minimo.pm is in libbio-perl-run-perl 1.7.1-3.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 | # BioPerl module for Bio::Tools::Run::Minimo
#
# Copyright Florent E Angly <florent-dot-angly-at-gmail-dot-com>
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Minimo - Wrapper for local execution of the Minimo assembler
=head1 SYNOPSIS
use Bio::Tools::Run::Minimo;
# Run Minmo using an input FASTA file
my $factory = Bio::Tools::Run::Minimo->new( -minimum_overlap_length => 35 );
my $asm_obj = $factory->run($fasta_file, $qual_file);
# An assembly object is returned by default
for my $contig ($assembly->all_contigs) {
... do something ...
}
# Read some sequences
use Bio::SeqIO;
my $sio = Bio::SeqIO->new(-file => $fasta_file, -format => 'fasta');
my @seqs;
while (my $seq = $sio->next_seq()) {
push @seqs,$seq;
}
# Run Minimo using input sequence objects and returning an assembly file
my $asm_file = 'results.ace';
$factory->out_type($asm_file);
$factory->run(\@seqs);
=head1 DESCRIPTION
Wrapper module for the local execution of the DNA assembly program Minimo.
Minimo is based on AMOS (http://sourceforge.net/apps/mediawiki/amos/) and
implements the same conservative assembly algorithm as Minimus
(http://sourceforge.net/apps/mediawiki/amos/index.php?title=Minimus).
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl
modules. Send your comments and suggestions preferably to one of the Bioperl
mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs
and their resolution. Bug reports can be submitted via the web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Florent E Angly
Email: florent-dot-angly-at-gmail-dot-com
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
=cut
package Bio::Tools::Run::Minimo;
use strict;
use IPC::Run;
use File::Copy;
use File::Spec;
use File::Basename;
use base qw( Bio::Root::Root Bio::Tools::Run::AssemblerBase );
our $program_name = 'Minimo'; # name of the executable
our @program_params = (qw( qual_in good_qual bad_qual min_len min_ident aln_wiggle out_prefix ace_exp ));
our @program_switches;
our %param_translation = (
'qual_in' => 'D QUAL_IN',
'good_qual' => 'D GOOD_QUAL',
'bad_qual' => 'D BAD_QUAL',
'min_len' => 'D MIN_LEN',
'min_ident' => 'D MIN_IDENT',
'aln_wiggle' => 'D ALN_WIGGLE',
'out_prefix' => 'D OUT_PREFIX',
'ace_exp' => 'D ACE_EXP'
);
our $qual_param = 'qual_in';
our $use_dash = 1;
our $join = '=';
our $asm_format = 'ace';
=head2 new
Title : new
Usage : $assembler->new( -min_len => 50,
-min_ident => 95 );
Function: Creates a Minimo factory
Returns : A Bio::Tools::Run::Minimo object
Args : Minimo options available in this module:
qual_in Input quality score file
good_qual Quality score to set for bases within the clear
range if no quality file was given (default: 30)
bad_qual Quality score to set for bases outside clear range
if no quality file was given (default: 10). If your
sequences are trimmed, try the same value as GOOD_QUAL.
min_len / minimum_overlap_length
Minimum contig overlap length (between 20 and 100 bp,
default: 35)
min_ident / minimum_overlap_similarity
Minimum contig overlap identity percentage (between 0
and 100 %, default: 98)
aln_wiggle Alignment wiggle value when determining the consensus
sequence (default: 2 bp)
out_prefix Prefix to use for the output file path and name
=cut
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->_set_program_options(\@args, \@program_params, \@program_switches,
\%param_translation, $qual_param, $use_dash, $join);
*minimum_overlap_length = \&min_len;
*minimum_overlap_similarity = \&min_ident;
$self->program_name($program_name) if not defined $self->program_name();
$self->_assembly_format($asm_format);
return $self;
}
=head2 out_type
Title : out_type
Usage : $factory->out_type('Bio::Assembly::ScaffoldI')
Function: Get/set the desired type of output
Returns : The type of results to return
Args : Desired type of results to return (optional):
'Bio::Assembly::IO' object
'Bio::Assembly::ScaffoldI' object (default)
The name of a file to save the results in
=cut
=head2 run
Title : run
Usage : $factory->run($fasta_file);
Function: Run TIGR Assembler
Returns : - a Bio::Assembly::ScaffoldI object, a Bio::Assembly::IO
object, a filename, or undef if all sequences were too small to
be usable
Returns : Assembly results (file, IO object or assembly object)
Args : - sequence input (FASTA file or sequence object arrayref)
- optional quality score input (QUAL file or quality score object
arrayref)
=cut
=head2 _run
Title : _run
Usage : $factory->_run()
Function: Make a system call and run TIGR Assembler
Returns : An assembly file
Args : - FASTA file
- optional QUAL file
=cut
sub _run {
my ($self, $fasta_file, $qual_file) = @_;
# qual_in Input quality score file
# fasta_exp Export results in FASTA format (0:no 1:yes, default: 1)
# ace_exp Export results in ACE format (0:no 1:yes, default: 1)
# Specify that we want an ACE output file
$self->ace_exp(1);
# Setup needed files and filehandles first
my ($output_fh, $output_file) = $self->_prepare_output_file( );
my ($stdout_fh, $stdout_file) = $self->io->tempfile( -dir => $self->tempdir() );
# Get program executable
my $exe = $self->executable;
# Get command-line options
my $options = $self->_translate_params();
# Usage: Minimo FASTA_IN [options]
# Options are of the style: -D PARAM=VAL
my @program_args = ( $exe, $fasta_file, @$options);
my @ipc_args = ( \@program_args, '>', $stdout_file);
# Print command for debugging
if ($self->verbose() >= 0) {
my $cmd = '';
$cmd .= join ( ' ', @program_args );
for ( my $i = 1 ; $i < scalar @ipc_args ; $i++ ) {
my $element = $ipc_args[$i];
my $ref = ref($element);
my $value;
if ( $ref && $ref eq 'SCALAR') {
$value = $$element;
} else {
$value = $element;
}
$cmd .= " $value";
}
$self->debug( "$exe command = $cmd\n" );
}
# Execute command
my $log_file = "$fasta_file.runAmos.log";
eval {
IPC::Run::run(@ipc_args) || die("There was a problem running $exe. The ".
"error message is: $!. Check the log file $log_file for possible causes.");
};
if ($@) {
$self->throw("$exe call crashed: $@");
}
# Close filehandles
close($output_fh);
close($stdout_fh);
# Result files
my $base = $self->out_prefix();
if (not defined $base) {
my $dirname = dirname($fasta_file);
my $basename = basename($fasta_file);
$basename =~ s/^(.+)\..+$/$1/;
$base = File::Spec->catfile($dirname, $basename);
}
my $ace_file = "$base-contigs.ace";
my $amos_file = "$base-contigs.afg";
# Remove all files except for the ACE file
for my $file ($log_file, $stdout_file, $amos_file) {
unlink $file;
}
# Clean the ACE file
$self->_clean_file($ace_file);
# Move the ACE file to its final destination
move ($ace_file, $output_file) or $self->throw("Could not move file ".
"'$ace_file' to '$output_file': $!");
return $output_file;
}
=head2 _clean_file
Title : _clean_file
Usage : $factory->_clean_file($file)
Function: Clean file in place by removing NULL characters. NULL characters
can be present in the output files of AMOS 2.0.8 but they do not
validate as proper sequence characters in Bioperl.
Returns : 1 for success
Args : Filename
=cut
sub _clean_file {
my ($self, $file) = @_;
# Set in-place file editing mode
local $^I = "~";
local @ARGV = ( $file );
# Replace lines in file
while (<>) {
s/\x0//g;
print;
}
return 1;
}
1;
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