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1 # $Id: psi.pm,v 1.6 2002/12/23 19:36:39 jason Exp $
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2 #
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3 # BioPerl module for Bio::AlignIO::psi
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4 #
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5 # Cared for by Jason Stajich <jason@bioperl.org>
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6 #
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7 # Copyright Jason Stajich
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::AlignIO::psi - Read/Write PSI-BLAST profile alignment files
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16
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17 =head1 SYNOPSIS
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18
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19 This module will parse PSI-BLAST output of the format seqid XXXX
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20
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21 =head1 DESCRIPTION
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22
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23 Describe the object here
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24
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25 =head1 FEEDBACK
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26
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27 =head2 Mailing Lists
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28
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29 User feedback is an integral part of the evolution of this and other
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30 Bioperl modules. Send your comments and suggestions preferably to
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31 the Bioperl mailing list. Your participation is much appreciated.
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32
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33 bioperl-l@bioperl.org - General discussion
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34 http://bioperl.org/MailList.shtml - About the mailing lists
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35
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36 =head2 Reporting Bugs
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37
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38 Report bugs to the Bioperl bug tracking system to help us keep track
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39 of the bugs and their resolution. Bug reports can be submitted via
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40 email or the web:
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41
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42 bioperl-bugs@bioperl.org
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43 http://bugzilla.bioperl.org/
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44
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45 =head1 AUTHOR - Jason Stajich
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46
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47 Email jason@bioperl.org
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48
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49 Describe contact details here
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50
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51 =head1 CONTRIBUTORS
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52
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53 Additional contributors names and emails here
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54
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55 =head1 APPENDIX
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56
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57 The rest of the documentation details each of the object methods.
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58 Internal methods are usually preceded with a _
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59
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60 =cut
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61
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62
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63 # Let the code begin...
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64
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65
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66 package Bio::AlignIO::psi;
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67 use vars qw(@ISA $BlockLen $IdLength);
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68 use strict;
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69
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70 $BlockLen = 100;
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71 $IdLength = 13;
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72
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73 # Object preamble - inherits from Bio::Root::Root
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74
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75 use Bio::SimpleAlign;
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76 use Bio::AlignIO;
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77 use Bio::LocatableSeq;
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78
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79 @ISA = qw(Bio::AlignIO);
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80
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81 =head2 new
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82
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83 Title : new
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84 Usage : my $obj = new Bio::AlignIO::psi();
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85 Function: Builds a new Bio::AlignIO::psi object
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86 Returns : Bio::AlignIO::psi
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87 Args :
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88
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89 =cut
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90
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91 =head2 next_aln
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92
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93 Title : next_aln
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94 Usage : $aln = $stream->next_aln()
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95 Function: returns the next alignment in the stream
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96 Returns : L<Bio::Align::AlignI> object
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97 Args : NONE
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98
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99 =cut
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100
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101 sub next_aln {
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102 my ($self) = @_;
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103 my $aln;
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104 my %seqs;
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105 my @order;
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106 while( defined ($_ = $self->_readline ) ) {
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107 next if( /^\s+$/);
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108 if( !defined $aln ) {
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109 $aln = new Bio::SimpleAlign;
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110 }
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111 my ($id,$s) = split;
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112 push @order, $id if( ! defined $seqs{$id});
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113 $seqs{$id} .= $s;
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114 }
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115 foreach my $id ( @order) {
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116 my $seq = new Bio::LocatableSeq(-seq => $seqs{$id},
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117 -id => $id,
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118 -start => 1,
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119 -end => length($seqs{$id}));
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120 $aln->add_seq($seq);
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121 }
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122 return $aln;
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123 }
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124
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125 =head2 write_aln
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126
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127 Title : write_aln
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128 Usage : $stream->write_aln(@aln)
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129 Function: writes the NCBI psi-format object (.aln) into the stream
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130 Returns : 1 for success and 0 for error
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131 Args : L<Bio::Align::AlignI> object
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132
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133
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134 =cut
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135
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136 sub write_aln {
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137 my ($self,$aln) = @_;
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138 unless( defined $aln && ref($aln) &&
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139 $aln->isa('Bio::Align::AlignI') ) {
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140 $self->warn("Must provide a valid Bio::Align::AlignI to write_aln");
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141 return 0;
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142 }
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143 my $ct = 0;
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144 my @seqs = $aln->each_seq;
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145 my $len = 1;
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146 my $alnlen = $aln->length;
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147 my $idlen = $IdLength;
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148 my @ids = map { substr($_->display_id,0,$idlen) } @seqs;
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149 while( $len < $alnlen ) {
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150 my $start = $len;
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151 my $end = $len + $BlockLen;
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152 if( $end > $alnlen ) { $end = $alnlen; }
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153 my $c = 0;
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154 foreach my $seq ( @seqs ) {
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155 $self->_print(sprintf("%-".$idlen."s %s\n",
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156 $ids[$c++],
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157 $seq->subseq($start,$end)));
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158 }
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159 $self->_print("\n");
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160 $len += $BlockLen+1;
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161 }
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162 $self->flush if $self->_flush_on_write && defined $self->_fh;
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163 return 1;
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164 }
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165
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166 1;
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