# $Id: embl.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::SeqIO::EMBL # # Please direct questions and support issues to # # Cared for by Ewan Birney # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::embl - EMBL sequence input/output stream =head1 SYNOPSIS It is probably best not to use this object directly, but rather go through the SeqIO handler system. Go: $stream = Bio::SeqIO->new(-file => $filename, -format => 'EMBL'); while ( (my $seq = $stream->next_seq()) ) { # do something with $seq } =head1 DESCRIPTION This object can transform Bio::Seq objects to and from EMBL flat file databases. There is a lot of flexibility here about how to dump things which should be documented more fully. There should be a common object that this and Genbank share (probably with Swissprot). Too much of the magic is identical. =head2 Optional functions =over 3 =item _show_dna() (output only) shows the dna or not =item _post_sort() (output only) provides a sorting func which is applied to the FTHelpers before printing =item _id_generation_func() This is function which is called as print "ID ", $func($annseq), "\n"; To generate the ID line. If it is not there, it generates a sensible ID line using a number of tools. If you want to output annotations in EMBL format they need to be stored in a Bio::Annotation::Collection object which is accessible through the Bio::SeqI interface method L. The following are the names of the keys which are polled from a L object. reference - Should contain Bio::Annotation::Reference objects comment - Should contain Bio::Annotation::Comment objects dblink - Should contain Bio::Annotation::DBLink objects =back =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 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://bugzilla.open-bio.org/ =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::embl; use vars qw(%FTQUAL_NO_QUOTE); use strict; use Bio::SeqIO::FTHelper; use Bio::SeqFeature::Generic; use Bio::Species; use Bio::Seq::SeqFactory; use Bio::Annotation::Collection; use Bio::Annotation::Comment; use Bio::Annotation::Reference; use Bio::Annotation::DBLink; use base qw(Bio::SeqIO); %FTQUAL_NO_QUOTE=( 'anticodon'=>1, 'citation'=>1, 'codon'=>1, 'codon_start'=>1, 'cons_splice'=>1, 'direction'=>1, 'evidence'=>1, 'label'=>1, 'mod_base'=> 1, 'number'=> 1, 'rpt_type'=> 1, 'rpt_unit'=> 1, 'transl_except'=> 1, 'transl_table'=> 1, 'usedin'=> 1, ); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); # hash for functions for decoding keys. $self->{'_func_ftunit_hash'} = {}; # sets this to one by default. People can change it $self->_show_dna(1); if ( ! defined $self->sequence_factory ) { $self->sequence_factory(Bio::Seq::SeqFactory->new (-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : =cut sub next_seq { my ($self,@args) = @_; my ($pseq,$c,$line,$name,$desc,$acc,$seqc,$mol,$div, $date, $comment, @date_arr); my ($annotation, %params, @features) = Bio::Annotation::Collection->new(); $line = $self->_readline; # This needs to be before the first eof() test if ( !defined $line ) { return; # no throws - end of file } if ( $line =~ /^\s+$/ ) { while ( defined ($line = $self->_readline) ) { $line =~/^\S/ && last; } # return without error if the whole next sequence was just a single # blank line and then eof return unless $line; } # no ID as 1st non-blank line, need short circuit and exit routine $self->throw("EMBL stream with no ID. Not embl in my book") unless $line =~ /^ID\s+\S+/; # At this point we are sure that $line contains an ID header line my $alphabet; if ( $line =~ tr/;/;/ == 6) { # New style headers contain exactly six semicolons. # New style header (EMBL Release >= 87, after June 2006) my $topology; my $sv; # ID DQ299383; SV 1; linear; mRNA; STD; MAM; 431 BP. # This regexp comes from the new2old.pl conversion script, from EBI if ($line =~ m/^ID (\w+);\s+SV (\d+); (\w+); ([^;]+); (\w{3}); (\w{3}); (\d+) BP./) { ($name, $sv, $topology, $mol, $div) = ($1, $2, $3, $4, $6); } if (defined($sv)) { $params{'-seq_version'} = $sv; $params{'-version'} = $sv; } if ($topology eq "circular") { $params{'-is_circular'} = 1; } if (defined $mol ) { if ($mol =~ /DNA/) { $alphabet='dna'; } elsif ($mol =~ /RNA/) { $alphabet='rna'; } elsif ($mol =~ /AA/) { $alphabet='protein'; } } } else { # Old style header (EMBL Release < 87, before June 2006) if ($line =~ /^ID\s+(\S+)[^;]*;\s+(\S+)[^;]*;\s+(\S+)[^;]*;/) { ($name, $mol, $div) = ($1, $2, $3); } if ($mol) { if ( $mol =~ /circular/ ) { $params{'-is_circular'} = 1; $mol =~ s|circular ||; } if (defined $mol ) { if ($mol =~ /DNA/) { $alphabet='dna'; } elsif ($mol =~ /RNA/) { $alphabet='rna'; } elsif ($mol =~ /AA/) { $alphabet='protein'; } } } } unless( defined $name && length($name) ) { $name = "unknown_id"; } # $self->warn("not parsing upper annotation in EMBL file yet!"); my $buffer = $line; local $_; BEFORE_FEATURE_TABLE : until ( !defined $buffer ) { $_ = $buffer; # Exit at start of Feature table if ( /^(F[HT]|SQ)/ ) { $self->_pushback($_) if( $1 eq 'SQ' || $1 eq 'FT'); last; } # Description line(s) if (/^DE\s+(\S.*\S)/) { $desc .= $desc ? " $1" : $1; } #accession number if ( /^AC\s+(.*)?/ || /^PA\s+(.*)?/) { my @accs = split(/[; ]+/, $1); # allow space in addition $params{'-accession_number'} = shift @accs unless defined $params{'-accession_number'}; push @{$params{'-secondary_accessions'}}, @accs; } #version number if ( /^SV\s+\S+\.(\d+);?/ ) { my $sv = $1; #$sv =~ s/\;//; $params{'-seq_version'} = $sv; $params{'-version'} = $sv; } #date (NOTE: takes last date line) if ( /^DT\s+(.+)$/ ) { my $line = $1; my ($date, $version) = split(' ', $line, 2); $date =~ tr/,//d; # remove comma if new version if ($version =~ /\(Rel\. (\d+), Created\)/xms ) { my $release = Bio::Annotation::SimpleValue->new( -tagname => 'creation_release', -value => $1 ); $annotation->add_Annotation($release); } elsif ($version =~ /\(Rel\. (\d+), Last updated, Version (\d+)\)/xms ) { my $release = Bio::Annotation::SimpleValue->new( -tagname => 'update_release', -value => $1 ); $annotation->add_Annotation($release); my $update = Bio::Annotation::SimpleValue->new( -tagname => 'update_version', -value => $2 ); $annotation->add_Annotation($update); } push @{$params{'-dates'}}, $date; } #keywords if ( /^KW (.*)\S*$/ ) { my @kw = split(/\s*\;\s*/,$1); push @{$params{'-keywords'}}, @kw; } # Organism name and phylogenetic information elsif (/^O[SC]/) { # pass the accession number so we can give an informative throw message if necessary my $species = $self->_read_EMBL_Species(\$buffer, $params{'-accession_number'}); $params{'-species'}= $species; } # NCBI TaxID Xref elsif (/^OX/) { my @links = $self->_read_EMBL_TaxID_DBLink(\$buffer); foreach my $dblink ( @links ) { $annotation->add_Annotation('dblink',$dblink); } } # References elsif (/^R/) { my @refs = $self->_read_EMBL_References(\$buffer); foreach my $ref ( @refs ) { $annotation->add_Annotation('reference',$ref); } } # DB Xrefs elsif (/^DR/) { my @links = $self->_read_EMBL_DBLink(\$buffer); foreach my $dblink ( @links ) { $annotation->add_Annotation('dblink',$dblink); } } # Comments elsif (/^CC\s+(.*)/) { $comment .= $1; $comment .= " "; while (defined ($_ = $self->_readline) ) { if (/^CC\s+(.*)/) { $comment .= $1; $comment .= " "; } else { last; } } my $commobj = Bio::Annotation::Comment->new(); $commobj->text($comment); $annotation->add_Annotation('comment',$commobj); $comment = ""; } # Get next line. $buffer = $self->_readline; } while ( defined ($_ = $self->_readline) ) { /^FT\s{3}\w/ && last; /^SQ / && last; /^CO / && last; } $buffer = $_; if (defined($buffer) && $buffer =~ /^FT /) { until ( !defined ($buffer) ) { my $ftunit = $self->_read_FTHelper_EMBL(\$buffer); # process ftunit my $feat = $ftunit->_generic_seqfeature($self->location_factory(), $name); # add taxon_id from source if available if ($params{'-species'} && ($feat->primary_tag eq 'source') && $feat->has_tag('db_xref') && (! $params{'-species'}->ncbi_taxid())) { foreach my $tagval ($feat->get_tag_values('db_xref')) { if (index($tagval,"taxon:") == 0) { $params{'-species'}->ncbi_taxid(substr($tagval,6)); last; } } } # add feature to list of features push(@features, $feat); if ( $buffer !~ /^FT/ ) { last; } } } # skip comments while ( defined ($buffer) && $buffer =~ /^XX/ ) { $buffer = $self->_readline(); } if ( $buffer =~ /^CO/ ) { until ( !defined ($buffer) ) { my $ftunit = $self->_read_FTHelper_EMBL(\$buffer); # process ftunit push(@features, $ftunit->_generic_seqfeature($self->location_factory(), $name)); if ( $buffer !~ /^CO/ ) { last; } } } if ( $buffer !~ /^SQ/ ) { while ( defined ($_ = $self->_readline) ) { /^SQ/ && last; } } $seqc = ""; while ( defined ($_ = $self->_readline) ) { m{^//} && last; $_ = uc($_); s/[^A-Za-z]//g; $seqc .= $_; } my $seq = $self->sequence_factory->create (-verbose => $self->verbose(), -division => $div, -seq => $seqc, -desc => $desc, -display_id => $name, -annotation => $annotation, -molecule => $mol, -alphabet => $alphabet, -features => \@features, %params); return $seq; } =head2 _write_ID_line Title : _write_ID_line Usage : $self->_write_ID_line($seq); Function: Writes the EMBL Release 87 format ID line to the stream, unless : there is a user-supplied ID line generation function in which : case that is used instead. : ( See Bio::SeqIO::embl::_id_generation_function(). ) Returns : nothing Args : Bio::Seq object =cut sub _write_ID_line { my ($self, $seq) = @_; my $id_line; # If there is a user-supplied ID generation function, use it. if ( $self->_id_generation_func ) { $id_line = "ID " . &{$self->_id_generation_func}($seq) . "\nXX\n"; } # Otherwise, generate a standard EMBL release 87 (June 2006) ID line. else { # The sequence name is supposed to be the primary accession number, my $name = $seq->accession_number(); if (!$name) { # but if it is not present, use the sequence ID. $name = $seq->id(); } $self->warn("No whitespace allowed in EMBL id [". $name. "]") if $name =~ /\s/; # Use the sequence version, or default to 1. my $version = $seq->version() || 1; my $len = $seq->length(); # Taxonomic division. my $div; if ( $seq->can('division') && defined($seq->division) && $self->_is_valid_division($seq->division) ) { $div = $seq->division(); } else { $div ||= 'UNC'; # 'UNC' is the EMBL division code for 'unclassified'. } my $mol; # If the molecule type is a valid EMBL type, use it. if ( $seq->can('molecule') && defined($seq->molecule) && $self->_is_valid_molecule_type($seq->molecule) ) { $mol = $seq->molecule(); } # Otherwise, choose unassigned DNA or RNA based on the alphabet. elsif ($seq->can('primary_seq') && defined $seq->primary_seq->alphabet) { my $alphabet =$seq->primary_seq->alphabet; if ($alphabet eq 'dna') { $mol ='unassigned DNA'; } elsif ($alphabet eq 'rna') { $mol='unassigned RNA'; } elsif ($alphabet eq 'protein') { $self->warn("Protein sequence found; EMBL is a nucleotide format."); $mol='AA'; # AA is not a valid EMBL molecule type. } } my $topology = 'linear'; if ($seq->is_circular) { $topology = 'circular'; } $mol ||= ''; # 'unassigned'; ? $id_line = "ID $name; SV $version; $topology; $mol; STD; $div; $len BP.\nXX\n"; $self->_print($id_line); } } =head2 _is_valid_division Title : _is_valid_division Usage : $self->_is_valid_division($div) Function: tests division code for validity Returns : true if $div is a valid EMBL release 87 taxonomic division. Args : taxonomic division code string =cut sub _is_valid_division { my ($self, $division) = @_; my %EMBL_divisions = ( "PHG" => 1, # Bacteriophage "ENV" => 1, # Environmental Sample "FUN" => 1, # Fungal "HUM" => 1, # Human "INV" => 1, # Invertebrate "MAM" => 1, # Other Mammal "VRT" => 1, # Other Vertebrate "MUS" => 1, # Mus musculus "PLN" => 1, # Plant "PRO" => 1, # Prokaryote "ROD" => 1, # Other Rodent "SYN" => 1, # Synthetic "UNC" => 1, # Unclassified "VRL" => 1 # Viral ); return exists($EMBL_divisions{$division}); } =head2 _is_valid_molecule_type Title : _is_valid_molecule_type Usage : $self->_is_valid_molecule_type($mol) Function: tests molecule type for validity Returns : true if $mol is a valid EMBL release 87 molecule type. Args : molecule type string =cut sub _is_valid_molecule_type { my ($self, $moltype) = @_; my %EMBL_molecule_types = ( "genomic DNA" => 1, "genomic RNA" => 1, "mRNA" => 1, "tRNA" => 1, "rRNA" => 1, "snoRNA" => 1, "snRNA" => 1, "scRNA" => 1, "pre-RNA" => 1, "other RNA" => 1, "other DNA" => 1, "unassigned DNA" => 1, "unassigned RNA" => 1 ); return exists($EMBL_molecule_types{$moltype}); } =head2 write_seq Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object (must be seq) to the stream Returns : 1 for success and undef for error Args : array of 1 to n Bio::SeqI objects =cut sub write_seq { my ($self,@seqs) = @_; foreach my $seq ( @seqs ) { $self->throw("Attempting to write with no seq!") unless defined $seq; unless ( ref $seq && $seq->isa('Bio::SeqI' ) ) { $self->warn("$seq is not a SeqI compliant sequence object!") if $self->verbose >= 0; unless ( ref $seq && $seq->isa('Bio::PrimarySeqI' ) ) { $self->throw("$seq is not a PrimarySeqI compliant sequence object!"); } } my $str = $seq->seq || ''; # Write the ID line. $self->_write_ID_line($seq); # Write the accession line if present my( $acc ); { if ( my $func = $self->_ac_generation_func ) { $acc = &{$func}($seq); } elsif ( $seq->isa('Bio::Seq::RichSeqI') && defined($seq->accession_number) ) { $acc = $seq->accession_number; $acc = join("; ", $acc, $seq->get_secondary_accessions); } elsif ( $seq->can('accession_number') ) { $acc = $seq->accession_number; } if (defined $acc) { $self->_print("AC $acc;\n", "XX\n") || return; } } # Date lines my $switch=0; if ( $seq->can('get_dates') ) { my @dates = $seq->get_dates(); my $ct = 1; my $date_flag = 0; my ($cr) = $seq->annotation->get_Annotations("creation_release"); my ($ur) = $seq->annotation->get_Annotations("update_release"); my ($uv) = $seq->annotation->get_Annotations("update_version"); unless ($cr && $ur && $ur) { $date_flag = 1; } foreach my $dt (@dates) { if (!$date_flag) { $self->_write_line_EMBL_regex("DT ","DT ", $dt." (Rel. $cr, Created)", '\s+|$',80) if $ct == 1; $self->_write_line_EMBL_regex("DT ","DT ", $dt." (Rel. $ur, Last updated, Version $uv)", '\s+|$',80) if $ct == 2; } else { # other formats? $self->_write_line_EMBL_regex("DT ","DT ", $dt,'\s+|$',80); } $switch =1; $ct++; } if ($switch == 1) { $self->_print("XX\n") || return; } } # Description lines $self->_write_line_EMBL_regex("DE ","DE ",$seq->desc(),'\s+|$',80) || return; #' $self->_print( "XX\n") || return; # if there, write the kw line { my( $kw ); if ( my $func = $self->_kw_generation_func ) { $kw = &{$func}($seq); } elsif ( $seq->can('keywords') ) { $kw = $seq->keywords; } if (defined $kw) { $self->_write_line_EMBL_regex("KW ", "KW ", $kw, '\s+|$', 80) || return; #' $self->_print( "XX\n") || return; } } # Organism lines if ($seq->can('species') && (my $spec = $seq->species)) { my @class = $spec->classification(); shift @class; # get rid of species name. Some embl files include # the species name in the OC lines, but this seems # more like an error than something we need to # emulate my $OS = $spec->scientific_name; if ($spec->common_name) { $OS .= ' ('.$spec->common_name.')'; } $self->_print("OS $OS\n") || return; my $OC = join('; ', reverse(@class)) .'.'; $self->_write_line_EMBL_regex("OC ","OC ",$OC,'; |$',80) || return; if ($spec->organelle) { $self->_write_line_EMBL_regex("OG ","OG ",$spec->organelle,'; |$',80) || return; } $self->_print("XX\n") || return; } # Reference lines my $t = 1; if ( $seq->can('annotation') && defined $seq->annotation ) { foreach my $ref ( $seq->annotation->get_Annotations('reference') ) { $self->_print( "RN [$t]\n") || return; # Having no RP line is legal, but we need both # start and end for a valid location. if ($ref->comment) { $self->_write_line_EMBL_regex("RC ", "RC ", $ref->comment, '\s+|$', 80) || return; #' } my $start = $ref->start; my $end = $ref->end; if ($start and $end) { $self->_print( "RP $start-$end\n") || return; } elsif ($start or $end) { $self->throw("Both start and end are needed for a valid RP line.". " Got: start='$start' end='$end'"); } if (my $med = $ref->medline) { $self->_print( "RX MEDLINE; $med.\n") || return; } if (my $pm = $ref->pubmed) { $self->_print( "RX PUBMED; $pm.\n") || return; } my $authors = $ref->authors; $authors =~ s/([\w\.]) (\w)/$1#$2/g; # add word wrap protection char '#' $self->_write_line_EMBL_regex("RA ", "RA ", $authors . ";", '\s+|$', 80) || return; #' # If there is no title to the reference, it appears # as a single semi-colon. All titles must end in # a semi-colon. my $ref_title = $ref->title || ''; $ref_title =~ s/[\s;]*$/;/; $self->_write_line_EMBL_regex("RT ", "RT ", $ref_title, '\s+|$', 80) || return; #' $self->_write_line_EMBL_regex("RL ", "RL ", $ref->location, '\s+|$', 80) || return; #' $self->_print("XX\n") || return; $t++; } # DB Xref lines if (my @db_xref = $seq->annotation->get_Annotations('dblink') ) { for my $dr (@db_xref) { my $db_name = $dr->database; my $prim = $dr->primary_id; my $opt = $dr->optional_id || ''; my $line = $opt ? "$db_name; $prim; $opt." : "$db_name; $prim."; $self->_write_line_EMBL_regex("DR ", "DR ", $line, '\s+|$', 80) || return; #' } $self->_print("XX\n") || return; } # Comment lines foreach my $comment ( $seq->annotation->get_Annotations('comment') ) { $self->_write_line_EMBL_regex("CC ", "CC ", $comment->text, '\s+|$', 80) || return; #' $self->_print("XX\n") || return; } } # "\\s\+\|\$" ## FEATURE TABLE $self->_print("FH Key Location/Qualifiers\n") || return; $self->_print("FH\n") || return; my @feats = $seq->can('top_SeqFeatures') ? $seq->top_SeqFeatures : (); if ($feats[0]) { if ( defined $self->_post_sort ) { # we need to read things into an array. # Process. Sort them. Print 'em my $post_sort_func = $self->_post_sort(); my @fth; foreach my $sf ( @feats ) { push(@fth,Bio::SeqIO::FTHelper::from_SeqFeature($sf,$seq)); } @fth = sort { &$post_sort_func($a,$b) } @fth; foreach my $fth ( @fth ) { $self->_print_EMBL_FTHelper($fth) || return; } } else { # not post sorted. And so we can print as we get them. # lower memory load... foreach my $sf ( @feats ) { my @fth = Bio::SeqIO::FTHelper::from_SeqFeature($sf,$seq); foreach my $fth ( @fth ) { if ( $fth->key eq 'CONTIG') { $self->_show_dna(0); } $self->_print_EMBL_FTHelper($fth) || return; } } } } if ( $self->_show_dna() == 0 ) { $self->_print( "//\n") || return; return; } $self->_print( "XX\n") || return; # finished printing features. $str =~ tr/A-Z/a-z/; # Count each nucleotide my $alen = $str =~ tr/a/a/; my $clen = $str =~ tr/c/c/; my $glen = $str =~ tr/g/g/; my $tlen = $str =~ tr/t/t/; my $len = $seq->length(); my $olen = $seq->length() - ($alen + $tlen + $clen + $glen); if ( $olen < 0 ) { $self->warn("Weird. More atgc than bases. Problem!"); } $self->_print("SQ Sequence $len BP; $alen A; $clen C; $glen G; $tlen T; $olen other;\n") || return; my $nuc = 60; # Number of nucleotides per line my $whole_pat = 'a10' x 6; # Pattern for unpacking a whole line my $out_pat = 'A11' x 6; # Pattern for packing a line my $length = length($str); # Calculate the number of nucleotides which fit on whole lines my $whole = int($length / $nuc) * $nuc; # Print the whole lines my( $i ); for ($i = 0; $i < $whole; $i += $nuc) { my $blocks = pack $out_pat, unpack $whole_pat, substr($str, $i, $nuc); $self->_print(sprintf(" $blocks%9d\n", $i + $nuc)) || return; } # Print the last line if (my $last = substr($str, $i)) { my $last_len = length($last); my $last_pat = 'a10' x int($last_len / 10) .'a'. $last_len % 10; my $blocks = pack $out_pat, unpack($last_pat, $last); $self->_print(sprintf(" $blocks%9d\n", $length)) || return; # Add the length to the end } $self->_print( "//\n") || return; $self->flush if $self->_flush_on_write && defined $self->_fh; } return 1; } =head2 _print_EMBL_FTHelper Title : _print_EMBL_FTHelper Usage : Function: Internal function Returns : 1 if writing suceeded, otherwise undef Args : =cut sub _print_EMBL_FTHelper { my ($self,$fth) = @_; if ( ! ref $fth || ! $fth->isa('Bio::SeqIO::FTHelper') ) { $fth->warn("$fth is not a FTHelper class. Attempting to print, but there could be tears!"); } #$self->_print( "FH Key Location/Qualifiers\n"); #$self->_print( sprintf("FT %-15s %s\n",$fth->key,$fth->loc)); # let if ( $fth->key eq 'CONTIG' ) { $self->_print("XX\n") || return; $self->_write_line_EMBL_regex("CO ", "CO ",$fth->loc, '\,|$',80) || return; #' return 1; } $self->_write_line_EMBL_regex(sprintf("FT %-15s ",$fth->key), "FT ",$fth->loc, '\,|$',80) || return; #' foreach my $tag ( keys %{$fth->field} ) { if ( ! defined $fth->field->{$tag} ) { next; } foreach my $value ( @{$fth->field->{$tag}} ) { $value =~ s/\"/\"\"/g; if ($value eq "_no_value") { $self->_write_line_EMBL_regex("FT ", "FT ", "/$tag",'.|$',80) || return; #' } # there are almost 3x more quoted qualifier values and they # are more common too so we take quoted ones first elsif (!$FTQUAL_NO_QUOTE{$tag}) { my $pat = $value =~ /\s/ ? '\s|\-|$' : '.|\-|$'; $self->_write_line_EMBL_regex("FT ", "FT ", "/$tag=\"$value\"",$pat,80) || return; } else { $self->_write_line_EMBL_regex("FT ", "FT ", "/$tag=$value",'.|$',80) || return; #' } } } return 1; } #' =head2 _read_EMBL_References Title : _read_EMBL_References Usage : Function: Reads references from EMBL format. Internal function really Example : Returns : Args : =cut sub _read_EMBL_References { my ($self,$buffer) = @_; my (@refs); # assume things are starting with RN if ( $$buffer !~ /^RN/ ) { warn("Not parsing line '$$buffer' which maybe important"); } my $b1; my $b2; my $title; my $loc; my $au; my $med; my $pm; my $com; while ( defined ($_ = $self->_readline) ) { /^R/ || last; /^RP (\d+)-(\d+)/ && do {$b1=$1;$b2=$2;}; /^RX MEDLINE;\s+(\d+)/ && do {$med=$1}; /^RX PUBMED;\s+(\d+)/ && do {$pm=$1}; /^RA (.*)/ && do { $au = $self->_concatenate_lines($au,$1); next; }; /^RT (.*)/ && do { $title = $self->_concatenate_lines($title,$1); next; }; /^RL (.*)/ && do { $loc = $self->_concatenate_lines($loc,$1); next; }; /^RC (.*)/ && do { $com = $self->_concatenate_lines($com,$1); next; }; } my $ref = Bio::Annotation::Reference->new(); $au =~ s/;\s*$//g; $title =~ s/;\s*$//g; $ref->start($b1); $ref->end($b2); $ref->authors($au); $ref->title($title); $ref->location($loc); $ref->medline($med); $ref->comment($com); $ref->pubmed($pm); push(@refs,$ref); $$buffer = $_; return @refs; } =head2 _read_EMBL_Species Title : _read_EMBL_Species Usage : Function: Reads the EMBL Organism species and classification lines. Example : Returns : A Bio::Species object Args : a reference to the current line buffer, accession number =cut sub _read_EMBL_Species { my( $self, $buffer, $acc ) = @_; my $org; $_ = $$buffer; my( $sub_species, $species, $genus, $common, $sci_name, $class_lines ); while (defined( $_ ||= $self->_readline )) { if (/^OS\s+(.+)/) { $sci_name .= ($sci_name) ? ' '.$1 : $1; } elsif (s/^OC\s+(.+)$//) { $class_lines .= $1; } elsif (/^OG\s+(.*)/) { $org = $1; } else { last; } $_ = undef; # Empty $_ to trigger read of next line } # $$buffer = $_; $self->_pushback($_); $sci_name =~ s{\.$}{}; $sci_name || return; # Convert data in classification lines into classification array. # only split on ';' or '.' so that classification that is 2 or more words # will still get matched, use map() to remove trailing/leading/intervening # spaces my @class = map { s/^\s+//; s/\s+$//; s/\s{2,}/ /g; $_; } split /(? Kingdom direction unless ($class[-1] eq $sci_name) { push(@class, $sci_name); } @class = reverse @class; # do minimal sanity checks before we hand off to Bio::Species which won't # be able to give informative throw messages if it has to throw because # of problems here $self->throw("$acc seems to be missing its OS line: invalid.") unless $sci_name; my %names; foreach my $i (0..$#class) { my $name = $class[$i]; $names{$name}++; if ($names{$name} > 1 && $name ne $class[$i - 1]) { $self->throw("$acc seems to have an invalid species classification."); } } my $make = Bio::Species->new(); $make->scientific_name($sci_name); $make->classification(@class); unless ($class[-1] eq 'Viruses') { $make->genus($genus) if $genus; $make->species($species) if $species; $make->sub_species($sub_species) if $sub_species; $make->common_name($common) if $common; } $make->organelle($org) if $org; return $make; } =head2 _read_EMBL_DBLink Title : _read_EMBL_DBLink Usage : Function: Reads the EMBL database cross reference ("DR") lines Example : Returns : A list of Bio::Annotation::DBLink objects Args : =cut sub _read_EMBL_DBLink { my( $self,$buffer ) = @_; my( @db_link ); $_ = $$buffer; while (defined( $_ ||= $self->_readline )) { if ( /^DR ([^\s;]+);\s*([^\s;]+);?\s*([^\s;]+)?\.$/) { my ($databse, $prim_id, $sec_id) = ($1,$2,$3); my $link = Bio::Annotation::DBLink->new(-database => $databse, -primary_id => $prim_id, -optional_id => $sec_id); push(@db_link, $link); } else { last; } $_ = undef; # Empty $_ to trigger read of next line } $$buffer = $_; return @db_link; } =head2 _read_EMBL_TaxID_DBLink Title : _read_EMBL_TaxID_DBLink Usage : Function: Reads the EMBL database cross reference to NCBI TaxID ("OX") lines Example : Returns : A list of Bio::Annotation::DBLink objects Args : =cut sub _read_EMBL_TaxID_DBLink { my( $self,$buffer ) = @_; my( @db_link ); $_ = $$buffer; while (defined( $_ ||= $self->_readline )) { if ( /^OX (\S+)=(\d+);$/ ) { my ($databse, $prim_id) = ($1,$2); my $link = Bio::Annotation::DBLink->new(-database => $databse, -primary_id => $prim_id,); push(@db_link, $link); } else { last; } $_ = undef; # Empty $_ to trigger read of next line } $$buffer = $_; return @db_link; } =head2 _filehandle Title : _filehandle Usage : $obj->_filehandle($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional) =cut sub _filehandle{ my ($obj,$value) = @_; if ( defined $value) { $obj->{'_filehandle'} = $value; } return $obj->{'_filehandle'}; } =head2 _read_FTHelper_EMBL Title : _read_FTHelper_EMBL Usage : _read_FTHelper_EMBL($buffer) Function: reads the next FT key line Example : Returns : Bio::SeqIO::FTHelper object Args : filehandle and reference to a scalar =cut sub _read_FTHelper_EMBL { my ($self,$buffer) = @_; my ($key, # The key of the feature $loc, # The location line from the feature @qual, # An arrray of lines making up the qualifiers ); if ($$buffer =~ /^FT\s{3}(\S+)\s+(\S+)/ ) { $key = $1; $loc = $2; # Read all the lines up to the next feature while ( defined($_ = $self->_readline) ) { if (/^FT(\s+)(.+?)\s*$/) { # Lines inside features are preceeded by 19 spaces # A new feature is preceeded by 3 spaces if (length($1) > 4) { # Add to qualifiers if we're in the qualifiers if (@qual) { push(@qual, $2); } # Start the qualifier list if it's the first qualifier elsif (substr($2, 0, 1) eq '/') { @qual = ($2); } # We're still in the location line, so append to location else { $loc .= $2; } } else { # We've reached the start of the next feature last; } } else { # We're at the end of the feature table last; } } } elsif ( $$buffer =~ /^CO\s+(\S+)/) { $key = 'CONTIG'; $loc = $1; # Read all the lines up to the next feature while ( defined($_ = $self->_readline) ) { if (/^CO\s+(\S+)\s*$/) { $loc .= $1; } else { # We've reached the start of the next feature last; } } } else { # No feature key return; } # Put the first line of the next feature into the buffer $$buffer = $_; # Make the new FTHelper object my $out = Bio::SeqIO::FTHelper->new(); $out->verbose($self->verbose()); $out->key($key); $out->loc($loc); # Now parse and add any qualifiers. (@qual is kept # intact to provide informative error messages.) QUAL: for (my $i = 0; $i < @qual; $i++) { $_ = $qual[$i]; my( $qualifier, $value ) = m{^/([^=]+)(?:=(.+))?} or $self->throw("Can't see new qualifier in: $_\nfrom:\n" . join('', map "$_\n", @qual)); if (defined $value) { # Do we have a quoted value? if (substr($value, 0, 1) eq '"') { # Keep adding to value until we find the trailing quote # and the quotes are balanced QUOTES: while ($value !~ /"$/ or $value =~ tr/"/"/ % 2) { #" $i++; my $next = $qual[$i]; if (!defined($next)) { $self->warn("Unbalanced quote in:\n".join("\n", @qual). "\nAdding quote to close...". "Check sequence quality!"); $value .= '"'; last QUOTES; } # Join to value with space if value or next line contains a space $value .= (grep /\s/, ($value, $next)) ? " $next" : $next; } # Trim leading and trailing quotes $value =~ s/^"|"$//g; # Undouble internal quotes $value =~ s/""/"/g; #" } } else { $value = '_no_value'; } # Store the qualifier $out->field->{$qualifier} ||= []; push(@{$out->field->{$qualifier}},$value); } return $out; } =head2 _write_line_EMBL Title : _write_line_EMBL Usage : Function: internal function Example : Returns : 1 if writing suceeded, else undef Args : =cut sub _write_line_EMBL { my ($self,$pre1,$pre2,$line,$length) = @_; $length || $self->throw("Miscalled write_line_EMBL without length. Programming error!"); my $subl = $length - length $pre2; my $linel = length $line; my $i; my $sub = substr($line,0,$length - length $pre1); $self->_print( "$pre1$sub\n") || return; for ($i= ($length - length $pre1);$i < $linel;) { $sub = substr($line,$i,($subl)); $self->_print( "$pre2$sub\n") || return; $i += $subl; } return 1; } =head2 _write_line_EMBL_regex Title : _write_line_EMBL_regex Usage : Function: internal function for writing lines of specified length, with different first and the next line left hand headers and split at specific points in the text Example : Returns : nothing Args : file handle, first header, second header, text-line, regex for line breaks, total line length =cut sub _write_line_EMBL_regex { my ($self,$pre1,$pre2,$line,$regex,$length) = @_; #print STDOUT "Going to print with $line!\n"; $length || $self->throw("Programming error - called write_line_EMBL_regex without length."); my $subl = $length - (length $pre1) -1 ; my( @lines ); CHUNK: while($line) { foreach my $pat ($regex, '[,;\.\/-]\s|'.$regex, '[,;\.\/-]|'.$regex) { if ($line =~ m/^(.{1,$subl})($pat)(.*)/ ) { my $l = $1.$2; $l =~ s/#/ /g # remove word wrap protection char '#' if $pre1 eq "RA "; my $newl = $3; $line = substr($line,length($l)); # be strict about not padding spaces according to # genbank format $l =~ s/\s+$//; push(@lines, $l); next CHUNK; } } # if we get here none of the patterns matched $subl or less chars $self->warn("trouble dissecting \"$line\"\n into chunks ". "of $subl chars or less - this tag won't print right"); # insert a space char to prevent infinite loops $line = substr($line,0,$subl) . " " . substr($line,$subl); } my $s = shift @lines; ($self->_print("$pre1$s\n") || return) if $s; foreach my $s ( @lines ) { $self->_print("$pre2$s\n") || return; } return 1; } =head2 _post_sort Title : _post_sort Usage : $obj->_post_sort($newval) Function: Returns : value of _post_sort Args : newvalue (optional) =cut sub _post_sort{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_post_sort'} = $value; } return $obj->{'_post_sort'}; } =head2 _show_dna Title : _show_dna Usage : $obj->_show_dna($newval) Function: Returns : value of _show_dna Args : newvalue (optional) =cut sub _show_dna{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_show_dna'} = $value; } return $obj->{'_show_dna'}; } =head2 _id_generation_func Title : _id_generation_func Usage : $obj->_id_generation_func($newval) Function: Returns : value of _id_generation_func Args : newvalue (optional) =cut sub _id_generation_func{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_id_generation_func'} = $value; } return $obj->{'_id_generation_func'}; } =head2 _ac_generation_func Title : _ac_generation_func Usage : $obj->_ac_generation_func($newval) Function: Returns : value of _ac_generation_func Args : newvalue (optional) =cut sub _ac_generation_func{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_ac_generation_func'} = $value; } return $obj->{'_ac_generation_func'}; } =head2 _sv_generation_func Title : _sv_generation_func Usage : $obj->_sv_generation_func($newval) Function: Returns : value of _sv_generation_func Args : newvalue (optional) =cut sub _sv_generation_func{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_sv_generation_func'} = $value; } return $obj->{'_sv_generation_func'}; } =head2 _kw_generation_func Title : _kw_generation_func Usage : $obj->_kw_generation_func($newval) Function: Returns : value of _kw_generation_func Args : newvalue (optional) =cut sub _kw_generation_func{ my $obj = shift; if ( @_ ) { my $value = shift; $obj->{'_kw_generation_func'} = $value; } return $obj->{'_kw_generation_func'}; } 1;