lib/Bio/SearchIO/cross_match.pm

   1 #
   2 # BioPerl module for Bio::SearchIO::cross_match
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Shin Leong <sleong@watson.wustl.edu>
   7 #
   8 # Copyright Shin Leong
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::SearchIO::cross_match - CrossMatch-specific subclass of Bio::SearchIO
  17
  18 =head1 SYNOPSIS
  19
  20     # Working with iterations (CrossMatch results)
  21     my $searchIO = Bio::SearchIO->new( -format => 'cross_match',
  22                             -file   => "$file.screen.out" )
  23     while(my $r = $searchIO->next_result) {
  24       while(my $hit = $r->next_hit) {
  25               while(my $hsp = $hit->next_hsp) {
  26            #Do the processing here.
  27         }
  28       }
  29     }
  30
  31 See L<Bio::SearchIO> for details about working with Bio::SearchIO.
  32
  33 =head1 DESCRIPTION
  34
  35 This object is a subclass of Bio::SearchIO
  36 and provides some operations that facilitate working with CrossMatch
  37 and CrossMatch results.
  38
  39 For general information about working with Results, see
  40 L<Bio::Search::Result::GenericResult>.
  41
  42 =head1 FEEDBACK
  43
  44 =head2 Mailing Lists
  45
  46 User feedback is an integral part of the evolution of this and other
  47 Bioperl modules. Send your comments and suggestions preferably to
  48 the Bioperl mailing list.  Your participation is much appreciated.
  49
  50   bioperl-l@bioperl.org                  - General discussion
  51   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  52
  53 =head2 Support
  54
  55 Please direct usage questions or support issues to the mailing list:
  56
  57 I<bioperl-l@bioperl.org>
  58
  59 rather than to the module maintainer directly. Many experienced and
  60 reponsive experts will be able look at the problem and quickly
  61 address it. Please include a thorough description of the problem
  62 with code and data examples if at all possible.
  63
  64 =head2 Reporting Bugs
  65
  66 Report bugs to the Bioperl bug tracking system to help us keep track
  67 of the bugs and their resolution. Bug reports can be submitted via the
  68 web:
  69
  70   https://github.com/bioperl/bioperl-live/issues
  71
  72 =head1 AUTHOR - Shin Leong
  73
  74 Email sleong@watson.wustl.edu
  75
  76 =head1 CONTRIBUTORS
  77
  78 Additional contributors names and emails here
  79
  80 =head1 APPENDIX
  81
  82 The rest of the documentation details each of the object methods.
  83 Internal methods are usually preceded with a _
  84
  85 =cut
  86
  87
  88 # Let the code begin...
  89
  90 package Bio::SearchIO::cross_match;
  91 use Bio::Search::Result::CrossMatchResult;
  92 use Bio::SearchIO;
  93 use Bio::Search::Hit::GenericHit;
  94 use Bio::Search::HSP::GenericHSP;
  95 use base qw(Bio::SearchIO);
  96
  97 =head2 next_result
  98
  99  Title   : next_result
 100  Usage   : $result = stream->next_result
 101  Function: Reads the next ResultI object from the stream and returns it.
 102
 103            Certain driver modules may encounter entries in the stream that
 104            are either misformatted or that use syntax not yet understood
 105            by the driver. If such an incident is recoverable, e.g., by
 106            dismissing a feature of a feature table or some other non-mandatory
 107            part of an entry, the driver will issue a warning. In the case
 108            of a non-recoverable situation an exception will be thrown.
 109            Do not assume that you can resume parsing the same stream after
 110            catching the exception. Note that you can always turn recoverable
 111            errors into exceptions by calling $stream->verbose(2) (see
 112            Bio::Root::RootI POD page).
 113  Returns : A Bio::Search::Result::ResultI object
 114  Args    : n/a
 115
 116 See L<Bio::Root::RootI>
 117
 118 =cut
 119
 120 sub next_result {
 121     my ($self) = @_;
 122     my $start = 0;
 123     while ( defined( $_ = $self->_readline ) ) {
 124         return if ( $self->{'_end_document'} );
 125         if (/^cross_match version\s+(.*?)$/) {
 126             $self->{_algorithm_version} = $1;
 127         }
 128         elsif (/^Maximal single base matches/) {
 129             $start = 1;
 130         }
 131         elsif (/^(\d+) matching entries/) {
 132             $self->{'_end_document'} = 1;
 133             return;
 134         }
 135         elsif ( ( $start || $self->{'_result_count'} ) && /^\s*(\d+)/xms ) {
 136             $self->{'_result_count'}++;
 137             return $self->_parse($_);
 138         }
 139         elsif ( !$self->{_parameters} ) {
 140             if (/.*?\s+(\-.*?)$/) {
 141                 my $p = $1;
 142                 my @pp = split /\s+/, $p;
 143                 for ( my $i = 0 ; $i < @pp ; $i++ ) {
 144                     if ( $pp[$i] =~ /^\-/ ) {
 145                         if ( $pp[ $i + 1 ] && $pp[ $i + 1 ] !~ /^\-/ ) {
 146                             $self->{_parameters}->{ $pp[$i] } = $pp[ $i + 1 ];
 147                             $i++;
 148                         }
 149                         else {
 150                             $self->{_parameters}->{ $pp[$i] } = "";
 151                         }
 152                     }
 153                 }
 154             }
 155         }
 156         elsif (/^Query file(s):\s+(.*?)$/) {
 157             $self->{_query_name} = $1;
 158         }
 159         elsif (/^Subject file(s):\s+(.*?)$/) {
 160             $self->{_subject_name} = $2;
 161         }
 162     }
 163 }
 164
 165
 166 =head2 _alignment
 167
 168  Title   : _alignment
 169  Usage   : private
 170
 171 =cut
 172
 173 sub _alignment {
 174     my $self = shift;
 175
 176 # C H_EO-aaa01PCR02    243 CCTCTGAATGGCTGAAGACCCCTCTGCCGAGGGAGGTTGGGGATTGTGGG 194
 177 #
 178 #   0284119_008.c1-      1 CCTCTGAATGGCTGAAGACCCCTCTGCCGAGGGAGGTTGGGGATTGTGGG 50
 179 #
 180 # C H_EO-aaa01PCR02    193 ACAAGGTCCCTTGGTGCTGATGGCCTGAAGGGGCCTGAGCTGTGGGCAGA 144
 181 #
 182 #   0284119_008.c1-     51 ACAAGGTCCCTTGGTGCTGATGGCCTGAAGGGGCCTGAGCTGTGGGCAGA 100
 183 #
 184 # C H_EO-aaa01PCR02    143 TGCAGTTTTCTGTGGGCTTGGGGAACCTCTCACGTTGCTGTGTCCTGGTG 94
 185 #
 186 #   0284119_008.c1-    101 TGCAGTTTTCTGTGGGCTTGGGGAACCTCTCACGTTGCTGTGTCCTGGTG 150
 187 #
 188 # C H_EO-aaa01PCR02     93 AGCAGCCCGACCAATAAACCTGCTTTTCTAAAAGGATCTGTGTTTGATTG 44
 189 #
 190 #   0284119_008.c1-    151 AGCAGCCCGACCAATAAACCTGCTTTTCTAAAAGGATCTGTGTTTGATTG 200
 191 #
 192 # C H_EO-aaa01PCR02     43 TATTCTCTGAAGGCAGTTACATAGGGTTACAGAGG 9
 193 #
 194 #   0284119_008.c1-    201 TATTCTCTGAAGGCAGTTACATAGGGTTACAGAGG 235
 195
 196     # LSF: Should be the blank line. Otherwise error.
 197     my $blank = $self->_readline;
 198     unless ( $blank =~ /^\s*$/ ) {
 199         return;
 200     }
 201     my @data;
 202     my @pad;
 203     $count = 0;
 204     while ( defined( $_ = $self->_readline ) ) {
 205         $count = 0 if ( $count >= 3 );
 206         next if (/^$/);
 207         if (/^(C  \S+.*?\d+ )(\S+) \d+$|^(  \S+.*?\d+ )(\S+) \d+$$|^\s+$/) {
 208             $count++;
 209             if ( $1 || $3 ) {
 210                 $pad[$count] = $1 ? $1 : $3;
 211                 push @{ $data[$count] }, ( $2 ? $2 : $4 );
 212             }
 213             else {
 214                 if (/\s{$pad[0],$pad[0]}(.*?)$/) {
 215                     push @{ $data[$count] }, $1;
 216                 }
 217                 else {
 218                     $self->throw("Format error for the homology line [$_].");
 219                 }
 220             }
 221         }
 222         else {
 223             last;
 224         }
 225     }
 226     return @data;
 227 }
 228
 229
 230 =head2 _parse
 231
 232  Title   : _parse
 233  Usage   : private
 234
 235 =cut
 236
 237 sub _parse {
 238     my $self         = shift;
 239     my $line         = shift;
 240     my $is_alignment = 0;
 241     my ( $hit_seq, $homology_seq, $query_seq );
 242
 243 #  32  5.13 0.00 0.00  H_DO-0065PCR0005792_034a.b1-1      327   365 (165)  C 1111547847_forward   (0)    39     1
 244 #OR
 245 #ALIGNMENT   32  5.13 0.00 0.00  H_DO-0065PCR0005792_034a.b1-1      327   365 (165)  C 1111547847_forward   (0)    39     1
 246     $line =~ s/^\s+|\s+$//g;
 247     my @r = split /\s+/, $line;
 248     if ( $r[0] eq "ALIGNMENT" ) {
 249         $is_alignment = 1;
 250         shift @r;
 251         ( $hit_seq, $homology_seq, $query_seq ) = $self->_alignment();
 252     }
 253     my $subject_seq_id;
 254     my $query_seq_id  = $r[4];
 255     my $query_start   = $r[5];
 256     my $query_end     = $r[6];
 257     my $is_complement = 0;
 258     my $subject_start;
 259     my $subject_end;
 260
 261     if ( $r[8] eq "C" && $r[9] !~ /^\(\d+\)$/ ) {
 262         $subject_seq_id = $r[9];
 263         $is_complement  = 1;
 264         $subject_start  = $r[11];
 265         $subject_end    = $r[12];
 266     }
 267     else {
 268         $subject_seq_id = $r[8];
 269         $subject_start  = $r[9];
 270         $subject_end    = $r[10];
 271     }
 272     my $hit = Bio::Search::Hit::GenericHit->new(
 273         -name => $subject_seq_id,
 274         -hsps => [
 275             Bio::Search::HSP::GenericHSP->new(
 276                 -query_name   => $query_seq_id,
 277                 -query_start  => $query_start,
 278                 -query_end    => $query_end,
 279                 -hit_name     => $subject_seq_id,
 280                 -hit_start    => $subject_start,
 281                 -hit_end      => $subject_end,
 282                 -query_length => 0,
 283                 -hit_length   => 0,
 284                 -identical    => $r[0],
 285                 -conserved    => $r[0],
 286                 -query_seq    => $query_seq
 287                 ? ( join "", @$query_seq )
 288                 : "",    #query sequence portion of the HSP
 289                 -hit_seq => $hit_seq
 290                 ? ( join "", @$hit_seq )
 291                 : "",    #hit sequence portion of the HSP
 292                 -homology_seq => $homology_seq
 293                 ? ( join "", @$homology_seq )
 294                 : "",    #homology sequence for the HSP
 295                    #LSF: Need the direction, just to fool the GenericHSP module.
 296                 -algorithm => 'SW',
 297             )
 298         ],
 299     );
 300     my $result = Bio::Search::Result::CrossMatchResult->new(
 301         -query_name        => $self->{_query_name},
 302         -query_accession   => '',
 303         -query_description => '',
 304         -query_length      => 0,
 305         -database_name     => $self->{_subject_name},
 306         -database_letters  => 0,
 307         -database_entries  => 0,
 308         -parameters        => $self->{_parameters},
 309         -statistics        => {},
 310         -algorithm         => 'cross_match',
 311         -algorithm_version => $self->{_algorithm_version},
 312     );
 313     $result->add_hit($hit);
 314     return $result;
 315 }
 316
 317
 318 =head2 result_count
 319
 320  Title   : result_count
 321  Usage   : $num = $stream->result_count;
 322  Function: Gets the number of CrossMatch results that have been parsed.
 323  Returns : integer
 324  Args    : none
 325  Throws  : none
 326
 327 =cut
 328
 329 sub result_count {
 330     my $self = shift;
 331     return $self->{'_result_count'};
 332 }
 333
 334
 335 1;
 336 #$Header$