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1 # $Id: gcg.pm,v 1.21 2002/10/25 16:22:01 jason Exp $
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2 #
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3 # BioPerl module for Bio::SeqIO::gcg
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4 #
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5 # Cared for by Ewan Birney <birney@ebi.ac.uk>
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6 # and Lincoln Stein <lstein@cshl.org>
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7 #
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8 # Copyright Ewan Birney & Lincoln Stein
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9 #
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10 # You may distribute this module under the same terms as perl itself
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11 #
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12 # _history
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13 # October 18, 1999 Largely rewritten by Lincoln Stein
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14
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15 # POD documentation - main docs before the code
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16
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17 =head1 NAME
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18
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19 Bio::SeqIO::gcg - GCG sequence input/output stream
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20
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21 =head1 SYNOPSIS
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22
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23 Do not use this module directly. Use it via the Bio::SeqIO class.
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24
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25 =head1 DESCRIPTION
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26
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27 This object can transform Bio::Seq objects to and from GCG flat
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28 file databases.
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29
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30 =head1 FEEDBACK
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31
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32 =head2 Mailing Lists
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33
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34 User feedback is an integral part of the evolution of this
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35 and other Bioperl modules. Send your comments and suggestions preferably
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36 to one of the Bioperl mailing lists.
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37 Your participation is much appreciated.
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38
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39 bioperl-l@bioperl.org - General discussion
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40 http://www.bioperl.org/MailList.shtml - About the mailing lists
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41
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42 =head2 Reporting Bugs
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43
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44 Report bugs to the Bioperl bug tracking system to help us keep track
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45 the bugs and their resolution. Bug reports can be submitted via email
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46 or the web:
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47
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48 bioperl-bugs@bio.perl.org
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49 http://bugzilla.bioperl.org/
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50
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51 =head1 AUTHORS - Ewan Birney & Lincoln Stein
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52
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53 Email: E<lt>birney@ebi.ac.ukE<gt>
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54 E<lt>lstein@cshl.orgE<gt>
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55
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56 =head1 CONTRIBUTORS
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57
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58 Jason Stajich, jason@bioperl.org
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59
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60 =head1 APPENDIX
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61
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62 The rest of the documentation details each of the object
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63 methods. Internal methods are usually preceded with a _
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64
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65 =cut
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66
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67 # Let the code begin...
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68
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69 package Bio::SeqIO::gcg;
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70 use vars qw(@ISA);
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71 use strict;
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72
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73 use Bio::SeqIO;
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74 use Bio::Seq::SeqFactory;
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75
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76 @ISA = qw(Bio::SeqIO);
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77
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78 sub _initialize {
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79 my($self,@args) = @_;
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80 $self->SUPER::_initialize(@args);
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81 if( ! defined $self->sequence_factory ) {
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82 $self->sequence_factory(new Bio::Seq::SeqFactory
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83 (-verbose => $self->verbose(),
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84 -type => 'Bio::Seq::RichSeq'));
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85 }
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86 }
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87
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88 =head2 next_seq
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89
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90 Title : next_seq
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91 Usage : $seq = $stream->next_seq()
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92 Function: returns the next sequence in the stream
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93 Returns : Bio::Seq object
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94 Args :
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95
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96 =cut
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97
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98 sub next_seq {
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99 my ($self,@args) = @_;
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100 my($id,$type,$desc,$line,$chksum,$sequence,$date,$len);
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101
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102 while( defined($_ = $self->_readline()) ) {
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103
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104 ## Get the descriptive info (anything before the line with '..')
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105 unless( /\.\.$/ ) { $desc.= $_; }
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106 ## Pull ID, Checksum & Type from the line containing '..'
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107 /\.\.$/ && do { $line = $_; chomp;
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108 if(/Check\:\s(\d+)\s/) { $chksum = $1; }
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109 if(/Type:\s(\w)\s/) { $type = $1; }
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110 if(/(\S+)\s+Length/)
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111 { $id = $1; }
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112 if(/Length:\s+(\d+)\s+(\S.+\S)\s+Type/ )
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113 { $len = $1; $date = $2;}
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114 last;
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115 }
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116 }
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117 return if ( !defined $_);
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118 chomp($desc); # remove last "\n"
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119
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120 while( defined($_ = $self->_readline()) ) {
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121
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122 ## This is where we grab the sequence info.
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123
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124 if( /\.\.$/ ) {
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125 $self->throw("Looks like start of another sequence. See documentation. ");
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126 }
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127
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128 next if($_ eq "\n"); ## skip whitespace lines in formatted seq
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129 s/[^a-zA-Z]//g; ## remove anything that is not alphabet char
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130 # $_ = uc($_); ## uppercase sequence: NO. Keep the case. HL
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131 $sequence .= $_;
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132 }
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133 ##If we parsed out a checksum, we might as well test it
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134
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135 if(defined $chksum) {
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136 unless(_validate_checksum($sequence,$chksum)) {
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137 $self->throw("Checksum failure on parsed sequence.");
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138 }
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139 }
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140
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141 ## Remove whitespace from identifier because the constructor
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142 ## will throw a warning otherwise...
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143 if(defined $id) { $id =~ s/\s+//g;}
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144
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145 ## Turn our parsed "Type: N" or "Type: P" (if found) into the appropriate
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146 ## keyword that the constructor expects...
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147 if(defined $type) {
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148 if($type eq "N") { $type = "dna"; }
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149 if($type eq "P") { $type = "prot"; }
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150 }
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151
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152 return $self->sequence_factory->create(-seq => $sequence,
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153 -id => $id,
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154 -desc => $desc,
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155 -type => $type,
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156 -dates => [ $date ]
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157 );
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158 }
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159
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160 =head2 write_seq
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161
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162 Title : write_seq
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163 Usage : $stream->write_seq(@seq)
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164 Function: writes the formatted $seq object into the stream
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165 Returns : 1 for success and 0 for error
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166 Args : array of Bio::PrimarySeqI object
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167
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168
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169 =cut
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170
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171 sub write_seq {
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172 my ($self,@seq) = @_;
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173 for my $seq (@seq) {
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174 $self->throw("Did not provide a valid Bio::PrimarySeqI object")
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175 unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI');
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176
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177 my $str = $seq->seq;
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178 my $comment = $seq->desc;
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179 my $id = $seq->id;
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180 my $type = ( $seq->alphabet() =~ /[dr]na/i ) ? 'N' : 'P';
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181 my $timestamp;
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182
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183 if( $seq->can('get_dates') ) {
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184 ($timestamp) = $seq->get_dates;
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185 } else {
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186 $timestamp = localtime(time);
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187 }
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188 my($sum,$offset,$len,$i,$j,$cnt,@out);
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189
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190 $len = length($str);
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191 ## Set the offset if we have any non-standard numbering going on
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192 $offset=1;
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193 # checksum
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194 $sum = $self->GCG_checksum($seq);
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195
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196 #Output the sequence header info
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197 push(@out,"$comment\n");
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198 push(@out,"$id Length: $len $timestamp Type: $type Check: $sum ..\n\n");
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199
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200 #Format the sequence
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201 $i = $#out + 1;
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202 for($j = 0 ; $j < $len ; ) {
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203 if( $j % 50 == 0) {
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204 $out[$i] = sprintf("%8d ",($j+$offset)); #numbering
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205 }
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206 $out[$i] .= sprintf("%s",substr($str,$j,10));
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207 $j += 10;
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208 if( $j < $len && $j % 50 != 0 ) {
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209 $out[$i] .= " ";
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210 }elsif($j % 50 == 0 ) {
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211 $out[$i++] .= "\n\n";
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212 }
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213 }
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214 local($^W) = 0;
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215 if($j % 50 != 0 ) {
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216 $out[$i] .= "\n";
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217 }
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218 $out[$i] .= "\n";
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219 return unless $self->_print(@out);
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220 }
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221
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222 $self->flush if $self->_flush_on_write && defined $self->_fh;
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223 return 1;
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224 }
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225
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226 =head2 GCG_checksum
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227
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228 Title : GCG_checksum
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229 Usage : $cksum = $gcgio->GCG_checksum($seq);
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230 Function : returns a gcg checksum for the sequence specified
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231
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232 This method can also be called as a class method.
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233 Example :
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234 Returns : a GCG checksum string
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235 Argument : a Bio::PrimarySeqI implementing object
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236
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237 =cut
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238
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239 sub GCG_checksum {
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240 my ($self,$seqobj) = @_;
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241 my $index = 0;
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242 my $checksum = 0;
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243 my $char;
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244
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245 my $seq = $seqobj->seq();
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246 $seq =~ tr/a-z/A-Z/;
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247
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248 foreach $char ( split(/[\.\-]*/, $seq)) {
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249 $index++;
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250 $checksum += ($index * (unpack("c",$char) || 0) );
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251 if( $index == 57 ) {
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252 $index = 0;
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253 }
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254 }
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255
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256 return ($checksum % 10000);
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257 }
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258
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259 =head2 _validate_checksum
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260
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261 Title : _validate_checksum
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262 Usage : n/a - internal method
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263 Function: if parsed gcg sequence contains a checksum field
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264 : we compare it to a value computed here on the parsed
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265 : sequence. A checksum mismatch would indicate some
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266 : type of parsing failure occured.
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267 :
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268 Returns : 1 for success, 0 for failure
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269 Args : string containing parsed seq, value of parsed cheksum
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270
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271
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272 =cut
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273
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274 sub _validate_checksum {
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275 my($seq,$parsed_sum) = @_;
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276 my($i,$len,$computed_sum,$cnt);
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277
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278 $len = length($seq);
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279
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280 #Generate the GCG Checksum value
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281
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282 for($i=0; $i<$len ;$i++) {
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283 $cnt++;
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284 $computed_sum += $cnt * ord(substr($seq,$i,1));
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285 ($cnt == 57) && ($cnt=0);
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286 }
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287 $computed_sum %= 10000;
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288
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289 ## Compare and decide if success or failure
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290
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291 if($parsed_sum == $computed_sum) {
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292 return 1;
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293 } else { return 0; }
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294
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295
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296 }
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297
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298 1;
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