Bio::SeqIO
swiss
Summary
Bio::SeqIO::swiss - Swissprot sequence input/output stream
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
It is probably best not to use this object directly, but
rather go through the SeqIO handler system:
use Bio::SeqIO;
$stream = Bio::SeqIO->new(-file => $filename,
-format => 'swiss');
while ( my $seq = $stream->next_seq() ) {
# do something with $seq
}
Description
This object can transform Bio::Seq objects to and from Swiss-Pprot flat
file databases.
There is a lot of flexibility here about how to dump things which needs
to be documented.
A Uniprot/Swiss-Prot entry holds information on one protein
sequence. If that sequence is identical across genes and species, they
are all merged into one entry. This creates complex needs for several
annotation fields in swiss-prot format.
The latest syntax for GN line is described in the user manual:
http://www.expasy.ch/sprot/userman.html#GN_line
Each of the possibly multiple genes in an entry can have Name,
Synonyms (only if there is a name), OrderedLocusNames (names from
genomic sequences) and ORFNames (temporary or cosmid names). "Name"
here really means "symbol". This complexity is now dealt with the
following way:
A new Bio::AnnotationI class was created in order to store the
data in tag-value pairs. This class (Bio::Annotation::TagTree)
is stored in the Bio::Annotation::Collection object and is
accessed like all other annotations. The tag name is 'gene_name'.
There is a single Bio::Annotation::TagTree per sequence record, which
corresponds to the original class that stored this data
(Bio::Annotation::StructuredValue). Depending on how we progress
this may change to represent each group of gene names.
For now, to access the gene name tree annotation, one uses the below method:
my ($gene) = $seq->annotation->get_Annotations('gene_name');
If you are only interested in displaying the values, value() returns a
string with similar formatting.
There are several ways to get directly at the information you want if you
know the element (tag) for the data. For gene names all data is stored with
the element-tag pairs:
"element1=tag1, tag2, tag3; element2=tag4, tag5;"
This normally means the element will be 'Name', 'Synonyms', etc. and the
gene names the values. Using findval(), you can do the following:
# grab a flattened list of all gene names
my @names = $ann->findval('Name');
# or iterated through the nodes and grab the name for each group
for my $node ($ann->findnode('gene_name')) {
my @names = $node->findval('Name');
}
The current method for parsing gene name data (and reconstructing gene name
output) is very generic. This is somewhat preemptive if, for instance, UniProt
decides to update and add another element name to the current ones using the
same formatting layout. Under those circumstances, one can iterate through the
tag tree in a safe way and retrieve all node data like so.
# retrieve the gene name nodes (groups like names, synonyms, etc).
for my $ann ($seq->annotation->get_Annotations('gene_name')) {
# each gene name group
for my $node ($ann->findnode('gene_name')) {
print "Gene name:\n";
# each gene name node (tag => value pair)
for my $n ($node->children) {
print "\t".$n->element.": ".$n->children."\n";
}
}
}
For more uses see Bio::Annotation::TagTree.
Since Uniprot/Swiss-Prot format have been around for quite some time, the
parser is also able to read in the older GN line syntax where genes
are separated by AND and various symbols by OR. The first symbol is
taken to be the 'Name' and the remaining ones are stored as 'Synonyms'.
_show_dna()
(output only) shows the dna or not
_post_sort()
(output only) provides a sorting func which is applied to the FTHelpers
before printing
_id_generation_func()
This is function which is called as
print "ID ", $func($seq), "\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 Swissprot format they need to be
stored in a Bio::Annotation::Collection object which is accessible
through the Bio::SeqI interface method
annotation().
The following are the names of the keys which are polled from a
Bio::Annotation::Collection object.
reference - Should contain Bio::Annotation::Reference objects
comment - Should contain Bio::Annotation::Comment objects
dblink - Should contain Bio::Annotation::DBLink objects
gene_name - Should contain Bio::Annotation::SimpleValue object
Methods
Methods description
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args : |
Title : write_seq
Usage : $stream->write_seq($seq)
Function: writes the $seq object (must be seq) to the stream
Returns : 1 for success and 0 for error
Args : array of 1 to n Bio::SeqI objects |
Title : _generateCRCTable
Usage :
Function:
Example :
Returns :
Args : |
Title : _crc32
Usage :
Function:
Example :
Returns :
Args : |
Title : _crc64
Usage :
Function:
Example :
Returns :
Args : |
Title : _print_swissprot_FTHelper
Usage :
Function:
Example :
Returns :
Args : |
Title : _read_swissprot_References
Usage :
Function: Reads references from swissprot format. Internal function really
Example :
Returns :
Args : |
Title : _read_swissprot_Species
Usage :
Function: Reads the swissprot Organism species and classification
lines.
Able to deal with unconventional species names.
Example : OS Unknown prokaryotic organism
$genus = undef ; $species = Unknown prokaryotic organism
Returns : A Bio::Species object
Args : |
Title : _read_FTHelper_swissprot
Usage : _read_FTHelper_swissprot(\$buffer)
Function: reads the next FT key line
Example :
Returns : Bio::SeqIO::FTHelper object
Args : |
Title : _write_line_swissprot
Usage :
Function: internal function
Example :
Returns :
Args : |
Title : _write_line_swissprot_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 |
Title : _post_sort
Usage : $obj->_post_sort($newval)
Function:
Returns : value of _post_sort
Args : newvalue (optional) |
Title : _show_dna
Usage : $obj->_show_dna($newval)
Function:
Returns : value of _show_dna
Args : newvalue (optional) |
Title : _id_generation_func
Usage : $obj->_id_generation_func($newval)
Function:
Returns : value of _id_generation_func
Args : newvalue (optional) |
Title : _ac_generation_func
Usage : $obj->_ac_generation_func($newval)
Function:
Returns : value of _ac_generation_func
Args : newvalue (optional) |
Title : _sv_generation_func
Usage : $obj->_sv_generation_func($newval)
Function:
Returns : value of _sv_generation_func
Args : newvalue (optional) |
Title : _kw_generation_func
Usage : $obj->_kw_generation_func($newval)
Function:
Returns : value of _kw_generation_func
Args : newvalue (optional) |
Methods code
sub _initialize
{ my($self,@args) = @_;
$self->SUPER::_initialize(@args);
$self->{'_func_ftunit_hash'} = {};
$self->_show_dna(1);
if ( ! defined $self->sequence_factory ) {
$self->sequence_factory(Bio::Seq::SeqFactory->new
(-verbose => $self->verbose(),
-type => 'Bio::Seq::RichSeq'));
}} | sub next_seq
{ my ($self,@args) = @_;
my ($pseq,$c,$line,$name,$desc,$acc,$seqc,$mol,$div, $sptr,$seq_div,
$date,$comment,@date_arr);
my $genename = "";
my ($annotation, %params, @features) = ( Bio::Annotation::Collection->new());
local $_;
1 while defined($_ = $self->_readline) && /^\s+$/;
return unless defined $_ && /^ID\s/;
unless( m{^
ID \s+ #
(\S+) \s+ # $1 entryname
([^\s;]+); \s+ # $2 DataClass
(?:PRT;)? \s+ # Molecule Type (optional)
[0-9]+[ ]AA \. # Sequencelength (capture?)
$
}ox ) {
$self->throw("swissprot stream with no ID. Not swissprot in my book");
}
($name, $seq_div) = ($1, $2);
$params{'-namespace'} =
($seq_div eq 'Reviewed' || $seq_div eq 'STANDARD') ? 'Swiss-Prot' :
($seq_div eq 'Unreviewed' || $seq_div eq 'PRELIMINARY') ? 'TrEMBL' :
$seq_div;
my ($junk, $division) = split q(_), $name;
$params{'-division'} = $division;
$params{'-alphabet'} = 'protein';
$params{'-display_id'} = $name;
BEFORE_FEATURE_TABLE :
while ( defined($_ = $self->_readline) ) {
last if( /^(FT|SQ)/ );
if (/^DE\s+(\S.*\S)/) {
$desc .= $desc ? " $1" : $1;
}
elsif (/^GN\s+(.*)/) {
$genename .= " " if $genename;
$genename .= $1;
}
elsif ( /^AC\s+(.+)/) {
my @accs = split(/[; ]+/, $1);
$params{'-accession_number'} = shift @accs
unless defined $params{'-accession_number'};
push @{$params{'-secondary_accessions'}}, @accs;
}
elsif ( /^DT\s+(.*)/ ) {
my $line = $1;
my ($date, $version) = split(' ', $line, 2);
$date =~ tr/,//d;
if ($version =~ /\(Rel\. (\d+), Last sequence update\)/ ||
/sequence version (\d+)/) {
my $update = Bio::Annotation::SimpleValue->new
(-tagname => 'seq_update',
-value => $1
);
$annotation->add_Annotation($update);
} elsif ($version =~ /\(Rel\. (\d+), Last annotation update\)/ ||
/entry version (\d+)/) {
$params{'-version'} = $1;
}
push @{$params{'-dates'}}, $date;
}
elsif ( /^PE\s+(.*)/ ) {
my $line = $1;
$line =~ s/;\s*//;
my $evidence = Bio::Annotation::SimpleValue->new
(-tagname => 'evidence',
-value => $line
);
$annotation->add_Annotation($evidence);
}
elsif (/^O[SCG]/) {
my $species = $self->_read_swissprot_Species($_);
$params{'-species'}= $species;
}
elsif (/^R/) {
my $refs = $self->_read_swissprot_References($_);
foreach my $r (@$refs) {
$annotation->add_Annotation('reference',$r);
}
}
elsif (/^CC\s{3}(.*)/) {
$comment .= $1;
$comment .= "\n";
while (defined ($_ = $self->_readline) && /^CC\s{3}(.*)/ ) {
$comment .= $1 . "\n";
}
my $commobj = Bio::Annotation::Comment->new(-tagname => 'comment',
-text => $comment);
$annotation->add_Annotation('comment',$commobj);
$comment = "";
$self->_pushback($_);
}
elsif (/^DR\s+(\S+)\;\s+(\S+)\;\s+([^;]+)[\;\.](.*)$/) {
my ($database,$primaryid,$optional,$comment) = ($1,$2,$3,$4);
$comment =~ s/\.\s*$//;
$comment =~ s/^\s+//;
my $dblinkobj = Bio::Annotation::DBLink->new
(-database => $database,
-primary_id => $primaryid,
-optional_id => $optional,
-comment => $comment,
-tagname => 'dblink',
);
$annotation->add_Annotation('dblink',$dblinkobj);
}
elsif ( /^KW\s+(.*)$/ ) {
my @kw = split(/\s*\;\s*/,$1);
defined $kw[-1] && $kw[-1] =~ s/\.$//;
push @{$params{'-keywords'}}, @kw;
}
}
if ($genename) {
my @stags;
if ($genename =~ /\w=\w/) {
for my $n (split(m{\s+and\s+},$genename)) {
my @genenames;
for my $section (split(m{\s*;\s*},$n)) {
my ($tag, $rest) = split("=",$section);
$rest ||= '';
for my $val (split(m{\s*,\s*},$rest)) {
push @genenames, [$tag => $val];
}
}
push @stags, ['gene_name' =>\@ genenames];
}
} else {
for my $section (split(/ AND /, $genename)) {
my @genenames;
$section =~ s/[\(\)\.]//g;
my @names = split(m{\s+OR\s+}, $section);
push @genenames, ['Name' => shift @names];
push @genenames, map {['Synonyms' => $_]} @names;
push @stags, ['gene_name' =>\@ genenames]
}
}
my $gn = Bio::Annotation::TagTree->new(-tagname => 'gene_name',
-value => ['gene_names' =>\@ stags]);
$annotation->add_Annotation('gene_name', $gn);
}
FEATURE_TABLE :
while (defined $_ && /^FT/ ) {
my $ftunit = $self->_read_FTHelper_swissprot($_);
if ($ftunit) {
push(@features,
$ftunit->_generic_seqfeature($self->location_factory(),
$params{'-seqid'}, "SwissProt"));
} else {
$self->warn("failed to parse feature table line for seq " .
$params{'-display_id'}. "\n$_");
}
$_ = $self->_readline;
}
while ( defined($_) && ! /^SQ/ ) {
$_ = $self->_readline;
}
$seqc = "";
while ( defined ($_ = $self->_readline) ) {
last if m{^//};
s/[^A-Za-z]//g;
$seqc .= uc($_);
}
my $seq= $self->sequence_factory->create
(-verbose => $self->verbose,
%params,
-seq => $seqc,
-desc => $desc,
-features =>\@ features,
-annotation => $annotation,
);
$seq->annotation($annotation);
return $seq;} | sub write_seq
{ my ($self,@seqs) = @_;
foreach my $seq ( @seqs ) {
$self->throw("Attempting to write with no seq!") unless defined $seq;
if ( ! ref $seq || ! $seq->isa('Bio::SeqI') ) {
$self->warn(" $seq is not a SeqI compliant module. Attempting to dump, but may fail!");
}
my $i;
my $str = $seq->seq;
my $div;
my $ns = ($seq->can('namespace')) && $seq->namespace();
my $len = $seq->length();
if ( !$seq->can('division') || ! defined ($div = $seq->division()) ) {
$div = 'UNK';
}
if (defined($ns)) {
$div = ($ns eq 'Swiss-Prot') ? 'Reviewed' :
($ns eq 'TrEMBL') ? 'Unreviewed' :
$ns;
} else {
$ns = 'Swiss-Prot';
}
$self->warn("No whitespace allowed in SWISS-PROT display id [". $seq->display_id. "]")
if $seq->display_id =~ /\s/;
my $temp_line;
if ( $self->_id_generation_func ) {
$temp_line = &{$self->_id_generation_func}($seq);
} else {
$temp_line = sprintf ("%-24s%-12s%9d AA.",
$seq->display_id(), $div.';', $len);
}
$self->_print( "ID $temp_line\n");
local($^W) = 0;
if ( $self->_ac_generation_func ) {
$temp_line = &{$self->_ac_generation_func}($seq);
$self->_print( "AC $temp_line\n");
}
elsif ($seq->can('accession_number') ) {
my $ac_line = $seq->accession_number;
if ($seq->can('get_secondary_accessions') ) {
foreach my $sacc ($seq->get_secondary_accessions) {
$ac_line .= "; ". $sacc;;
}
$ac_line .= ";";
}
$self->_write_line_swissprot_regex("AC ","AC ",$ac_line,
"\\s\+\|\$",$LINE_LENGTH);
}
if ( $seq->can('get_dates') ) {
my @dates = $seq->get_dates();
my $ct = 1;
my $seq_version = $seq->version;
my ($update_version) = $seq->annotation->get_Annotations("seq_update");
foreach my $dt (@dates) {
$self->_write_line_swissprot_regex("DT ","DT ",
$dt.', integrated into UniProtKB/'.$ns.'.',
"\\s\+\|\$",$LINE_LENGTH) if $ct == 1;
$self->_write_line_swissprot_regex("DT ","DT ",
$dt.", sequence version ".$update_version->display_text.'.',
"\\s\+\|\$",$LINE_LENGTH) if $ct == 2;
$self->_write_line_swissprot_regex("DT ","DT ",
$dt.", entry version $seq_version.",
"\\s\+\|\$",$LINE_LENGTH) if $ct == 3;
$ct++;
}
}
$self->_write_line_swissprot_regex("DE ","DE ",$seq->desc(),"\\s\+\|\$",$LINE_LENGTH);
foreach my $gene ( my @genes = $seq->annotation->get_Annotations('gene_name') ) {
my @genelines;
for my $node ($gene->findnode('gene_name')) {
my $geneline = "GN ";
my %genedata = $node->hash;
for my $tag (@GENE_NAME_ORDER) {
if (exists $genedata{$tag}) {
$geneline .= (ref $genedata{$tag} eq 'ARRAY') ?
"$tag=".join(', ',@{$genedata{$tag}})."; " :
"$tag=$genedata{$tag}; ";
delete $genedata{$tag};
}
}
for my $tag (sort keys %genedata) {
$geneline .= (ref $genedata{$tag} eq 'ARRAY') ?
"$tag=".join(', ',@{$genedata{$tag}})."; " :
"$tag=$genedata{$tag}; ";
delete $genedata{$tag};
}
push @genelines, "$geneline\n";
}
$self->_print(join("GN and\n",@genelines));
}
if ($seq->can('species') && (my $spec = $seq->species)) {
my @class = $spec->classification();
shift(@class);
my $species = $spec->species;
my $genus = $spec->genus;
my $OS = $spec->scientific_name;
if ($class[-1] =~ /viruses/i) {
$OS = $species;
$OS .= " ". $spec->sub_species if $spec->sub_species;
}
foreach (($spec->variant, $spec->common_name)) {
$OS .= " ($_)" if $_;
}
$self->_print( "OS $OS.\n");
my $OC = join('; ', reverse(@class)) .'.';
$self->_write_line_swissprot_regex("OC ","OC ",$OC,"\;\|\$ ",$LINE_LENGTH);
if ($spec->organelle) {
$self->_write_line_swissprot_regex("OG ","OG ",$spec->organelle,"\;\|\$ ",$LINE_LENGTH);
}
if ($spec->ncbi_taxid) {
$self->_print("OX NCBI_TaxID=".$spec->ncbi_taxid.";\n");
}
}
my $t = 1;
foreach my $ref ( $seq->annotation->get_Annotations('reference') ) {
$self->_print( "RN [$t]\n");
if ($ref->rp) {
$self->_write_line_swissprot_regex("RP ","RP ",$ref->rp,
"\\s\+\|\$",$LINE_LENGTH);
}
if ($ref->comment) {
$self->_write_line_swissprot_regex("RC ","RC ",$ref->comment,
"\\s\+\|\$",$LINE_LENGTH);
}
if ($ref->medline or $ref->pubmed or $ref->doi) {
my $line;
$line .= "MEDLINE=". $ref->medline. '; ' if $ref->medline;
$line .= "PubMed=". $ref->pubmed. '; ' if $ref->pubmed;
$line .= "DOI=". $ref->doi. '; ' if $ref->doi;
chop $line;
$self->_write_line_swissprot_regex("RX ","RX ",
$line,
"\\s\+\|\$",$LINE_LENGTH);
}
my $author = $ref->authors .';' if($ref->authors);
my $title = $ref->title .';' if( $ref->title);
my $rg = $ref->rg . ';' if $ref->rg;
$author =~ s/([\w\.]) (\w)/$1#$2/g;
$self->_write_line_swissprot_regex("RG ","RG ",$rg,"\\s\+\|\$",$LINE_LENGTH) if $rg;
$self->_write_line_swissprot_regex("RA ","RA ",$author,"\\s\+\|\$",$LINE_LENGTH) if $author;
$self->_write_line_swissprot_regex("RT ","RT ",$title,'[\s\-]+|$',$LINE_LENGTH) if $title;
$self->_write_line_swissprot_regex("RL ","RL ",$ref->location,"\\s\+\|\$",$LINE_LENGTH);
$t++;
}
foreach my $comment ( $seq->annotation->get_Annotations('comment') ) {
foreach my $cline (split ("\n", $comment->text)) {
while (length $cline > 74) {
$self->_print("CC ",(substr $cline,0,74),"\n");
$cline = substr $cline,74;
}
$self->_print("CC ",$cline,"\n");
}
}
foreach my $dblink ( $seq->annotation->get_Annotations('dblink') ) {
my ($primary_id) = $dblink->primary_id;
if (defined($dblink->comment) && ($dblink->comment) ) {
$self->_print("DR ",$dblink->database,"; ",$primary_id,"; ",
$dblink->optional_id,"; ",$dblink->comment,".\n");
} elsif ($dblink->optional_id) {
$self->_print("DR ",$dblink->database,"; ",
$primary_id,"; ",
$dblink->optional_id,".\n");
} else {
$self->_print("DR ",$dblink->database,
"; ",$primary_id,"; ","-.\n");
}
}
foreach my $evidence ( $seq->annotation->get_Annotations('evidence') ) {
$self->_print("PE ",$evidence->value,";\n");
}
{
my $kw;
if ( my $func = $self->_kw_generation_func ) {
$kw = &{$func}($seq);
} elsif ( $seq->can('keywords') ) {
$kw = $seq->keywords;
if ( ref($kw) =~ /ARRAY/i ) {
$kw = join("; ", @$kw);
}
$kw .= '.' if $kw and $kw !~ /\.$/ ;
}
$kw =~ s/([\w\.]) (\w)/$1#$2/g;
$self->_write_line_swissprot_regex("KW ","KW ",
$kw, "\\s\+\|\$",$LINE_LENGTH)
if $kw;
}
my @feats = $seq->can('top_SeqFeatures') ? $seq->top_SeqFeatures : ();
if ($feats[0]) {
if ( defined $self->_post_sort ) {
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 ) {
$self->_print_swissprot_FTHelper($fth);
}
} else {
foreach my $sf ( @feats ) {
my @fth = Bio::SeqIO::FTHelper::from_SeqFeature($sf,$seq);
foreach my $fth ( @fth ) {
if ( ! $fth->isa('Bio::SeqIO::FTHelper') ) {
$sf->throw("Cannot process FTHelper... $fth");
}
$self->_print_swissprot_FTHelper($fth);
}
}
}
if ( $self->_show_dna() == 0 ) {
return;
}
}
my $mw = ${Bio::Tools::SeqStats->get_mol_wt($seq->primary_seq)}[0];
my $crc64 = $self->_crc64(\$str);
$self->_print( sprintf("SQ SEQUENCE %4d AA; %d MW; %16s CRC64;\n",
$len,$mw,$crc64));
$self->_print( " ");
my $linepos;
for ($i = 0; $i < length($str); $i += 10) {
$self->_print( " ", substr($str,$i,10));
$linepos += 11;
if ( ($i+10)%60 == 0 && (($i+10) < length($str))) {
$self->_print( "\n ");
}
}
$self->_print( "\n//\n");
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
}
} | sub _generateCRCTable
{
my $poly = 0xEDB88320;
my ($self) = shift;
$self->{'_crcTable'} = [];
foreach my $i (0..255) {
my $crc = $i;
for (my $j=8; $j > 0; $j--) {
if ($crc & 1) {
$crc = ($crc >> 1) ^ $poly;
} else {
$crc >>= 1;
}
}
${$self->{'_crcTable'}}[$i] = $crc;
} } | sub _crc32
{ my( $self, $str ) = @_;
$self->throw("Argument to crc32() must be ref to scalar")
unless ref($str) eq 'SCALAR';
$self->_generateCRCTable() unless exists $self->{'_crcTable'};
my $len = length($$str);
my $crc = 0xFFFFFFFF;
for (my $i = 0; $i < $len; $i++) {
my $int = ord uc substr $$str, $i, 1;
$crc = (($crc >> 8) & 0x00FFFFFF) ^
${$self->{'_crcTable'}}[ ($crc ^ $int) & 0xFF ];
}
return $crc;} | sub _crc64
{ my ($self, $sequence) = @_;
my $POLY64REVh = 0xd8000000;
my @CRCTableh = 256;
my @CRCTablel = 256;
my $initialized;
my $seq = $$sequence;
my $crcl = 0;
my $crch = 0;
if (!$initialized) {
$initialized = 1;
for (my $i=0; $i<256; $i++) {
my $partl = $i;
my $parth = 0;
for (my $j=0; $j<8; $j++) {
my $rflag = $partl & 1;
$partl >>= 1;
$partl |= (1 << 31) if $parth & 1;
$parth >>= 1;
$parth ^= $POLY64REVh if $rflag;
}
$CRCTableh[$i] = $parth;
$CRCTablel[$i] = $partl;
}
}
foreach (split '', $seq) {
my $shr = ($crch & 0xFF) << 24;
my $temp1h = $crch >> 8;
my $temp1l = ($crcl >> 8) | $shr;
my $tableindex = ($crcl ^ (unpack "C", $_)) & 0xFF;
$crch = $temp1h ^ $CRCTableh[$tableindex];
$crcl = $temp1l ^ $CRCTablel[$tableindex];
}
my $crc64 = sprintf("%08X%08X", $crch, $crcl);
return $crc64;
} | sub _print_swissprot_FTHelper
{ my ($self,$fth,$always_quote) = @_;
$always_quote ||= 0;
my ($start,$end) = ('?', '?');
if ( ! ref $fth || ! $fth->isa('Bio::SeqIO::FTHelper') ) {
$fth->warn("$fth is not a FTHelper class. ".
"Attempting to print, but there could be tears!");
}
my $desc = "";
for my $tag ( qw(description gene note product) ) {
if ( exists $fth->field->{$tag} ) {
$desc = @{$fth->field->{$tag}}[0].".";
last;
}
}
$desc =~ s/\.$//;
my $ftid = "";
if ( exists $fth->field->{'FTId'} ) {
$ftid = @{$fth->field->{'FTId'}}[0]. '.';
}
my $key =substr($fth->key,0,8);
my $loc = $fth->loc;
if ( $loc =~ /(\?|\d+|\>\d+|<\d+)?\.\.(\?|\d+|<\d+|>\d+)?/ ) {
$start = $1 if defined $1;
$end = $2 if defined $2;
} elsif ( $loc =~ /join\((\d+)((?:,\d+)+)?\)/) {
my @y = ($1);
if ( defined( my $m = $2) ) {
$m =~ s/^\,//;
push @y, split(/,/,$m);
}
for my $x ( @y ) {
$self->_write_line_swissprot_regex(
sprintf("FT %-8s %6s %6s ",
$key,
$x ,$x),
"FT ",
$desc.'.','\s+|$',$LINE_LENGTH);
}
return;
} else {
$start = $end = $fth->loc;
}
if ($desc) {
$self->_write_line_swissprot_regex(sprintf("FT %-8s %6s %6s ",
$key,
$start ,$end),
"FT ",
$desc. '.', '\s+|$', $LINE_LENGTH);
} else {
$self->_write_line_swissprot_regex(sprintf("FT %-8s %6s %6s",
$key,
$start ,$end),
"FT ",
' ', '\s+|$', $LINE_LENGTH);
}
if ($ftid) {
$self->_write_line_swissprot_regex("FT ",
"FT ",
"/FTId=$ftid",'.|$',$LINE_LENGTH);
}
}
} | sub _read_swissprot_References
{ my ($self,$line) = @_;
my ($b1, $b2, $rp, $rg, $title, $loc, $au, $med, $com, $pubmed, $doi);
my @refs;
local $_ = $line;
while ( defined $_ ) {
if ( /^[^R]/ || /^RN/ ) {
if ( $rp ) {
$rg =~ s/;\s*$//g if defined($rg);
if (defined($au)) {
$au =~ s/;\s*$//;
} else {
$au = $rg;
}
$title =~ s/;\s*$//g if defined($title);
push @refs, Bio::Annotation::Reference->new
(-title => $title,
-start => $b1,
-end => $b2,
-authors => $au,
-location=> $loc,
-medline => $med,
-pubmed => $pubmed,
-doi => $doi,
-comment => $com,
-rp => $rp,
-rg => $rg,
-tagname => 'reference',
);
$rp = '';
}
if (index($_,'R') != 0) {
$self->_pushback($_);
last;
}
$b1 = $b2 = $rg = $med = $com = $pubmed = $doi = undef;
$title = $loc = $au = undef;
} elsif ( /^RP\s{3}(.+? OF (\d+)-(\d+).*)/) {
$rp .= $1;
$b1 = $2;
$b2 = $3;
} elsif ( /^RP\s{3}(.*)/) {
if ($rp) {
$rp .= " ".$1;
} else {
$rp = $1;
}
} elsif (/^RX\s{3}(.*)/) {
my $line = $1;
$med = $1 if $line =~ /MEDLINE=(\d+);/;
$pubmed = $1 if $line =~ /PubMed=(\d+);/;
$doi = $1 if $line =~ /DOI=(.+);/;
} elsif ( /^RA\s{3}(.*)/ ) {
$au .= $au ? " $1" : $1;
} elsif ( /^RG\s{3}(.*)/ ) {
$rg .= $rg ? " $1" : $1;
} elsif ( /^RT\s{3}(.*)/ ) {
if ($title) {
my $tline = $1;
$title .= ($title =~ /[\w;,:\?!]$/) ? " $tline" : $tline;
} else {
$title = $1;
}
} elsif (/^RL\s{3}(.*)/ ) {
$loc .= $loc ? " $1" : $1;
} elsif ( /^RC\s{3}(.*)/ ) {
$com .= $com ? " $1" : $1;
}
$_ = $self->_readline;
}
return\@ refs;} | sub _read_swissprot_Species
{ my( $self,$line ) = @_;
my $org;
local $_ = $line;
my( $sub_species, $species, $genus, $common, $variant, $ncbi_taxid, $sci_name, $class_lines, $descr );
my $osline = "";
my $do_genus_check = 1;
while ( defined $_ ) {
last unless /^O[SCGX]/;
if (/^OS\s+(\S.+)/ && (! defined($sci_name))) {
$osline .= " " if $osline;
$osline .= $1;
if ($osline =~ s/(,|, and|\.)$//) {
if ($osline =~ /[^\(\)]+\(.+\)[^\(\)]+$/) {
$sci_name = $osline;
$sci_name =~ s/\.$//;
$descr = '';
$do_genus_check = 0;
} else {
($sci_name, $descr) = $osline =~ /(\S[^\(]+)(.*)/;
}
$sci_name =~ s/\s+$//;
while ($descr =~ /\(([^\)]+)\)/g) {
my $item = $1;
if ((! defined($variant)) &&
(($item =~ /(^|[^\(\w])([Ss]train|isolate|serogroup|serotype|subtype|clone)\b/) ||
($item =~ /^(biovar|pv\.|type\s+)/))) {
$variant = $item;
} elsif ($item =~ s/^subsp\.\s+//) {
if (! $sub_species) {
$sub_species = $item;
} elsif (! $variant) {
$variant = $item;
}
} elsif (! defined($common)) {
$common = $item;
if ((index($common, '(') >= 0) &&
(index($common, ')') < 0)) {
$common .= ')';
}
}
}
}
} elsif (s/^OC\s+(\S.+)$//) {
$class_lines .= $1;
} elsif (/^OG\s+(.*)/) {
$org = $1;
} elsif (/^OX\s+(.*)/ && (! defined($ncbi_taxid))) {
my $taxstring = $1;
if ($taxstring =~ /NCBI_TaxID=([\w\d]+)/) {
$ncbi_taxid = $1;
} else {
$self->throw("$taxstring doesn't look like NCBI_TaxID");
}
}
$_ = $self->_readline;
}
$self->_pushback($_);
$sci_name || return;
return if grep { $_ eq $sci_name } @Unknown_names;
$class_lines=~s/\.\s*$//;
my @class = map { s/^\s+//; s/\s+$//; s/\s{2,}/ /g; $_; } split /[;\.]*;/, $class_lines;
if ($class[0] =~ /viruses/i) {
my @virusnames = split(/\s+/, $sci_name);
$species = (@virusnames > 1) ? pop(@virusnames) : '';
$genus = join(" ", @virusnames);
$sub_species = $descr;
} elsif ($do_genus_check) {
my $possible_genus = $class[-1];
$possible_genus .= "|$class[-2]" if $class[-2];
if ($sci_name =~ /^($possible_genus)/) {
$genus = $1;
($species) = $sci_name =~ /^$genus\s+(.+)/;
} else {
$species = $sci_name;
}
if ($species && $species =~ /subsp\.|var\./) {
($species, $sub_species) = $species =~ /(.+)\s+((?:subsp\.|var\.).+)/;
}
}
unless ($class[-1] eq $sci_name) {
push(@class, $sci_name);
}
@class = reverse @class;
my $taxon = Bio::Species->new();
$taxon->scientific_name($sci_name);
$taxon->classification(@class);
$taxon->common_name($common) if $common;
$taxon->sub_species($sub_species) if $sub_species;
$taxon->organelle($org) if $org;
$taxon->ncbi_taxid($ncbi_taxid) if $ncbi_taxid;
$taxon->variant($variant) if $variant;
return $taxon;} | sub _read_FTHelper_swissprot
{ my ($self,$line ) = @_;
local $_ = $line;
my ($key,
$loc,
$desc,
$ftid,
);
if ( m/^FT\s{3}(\w+)\s+([\d\?\<]+)\s+([\d\?\>]+)\s*(.*)$/ox) {
$key = $1;
my $loc1 = $2;
my $loc2 = $3;
$loc = "$loc1..$loc2";
if ($4 && (length($4) > 0)) {
$desc = $4;
chomp($desc);
} else {
$desc = "";
}
}
while ( defined($_ = $self->_readline) && /^FT\s{20,}(\S.*)$/ ) {
my $continuation_line = $1;
if ( $continuation_line =~ /.FTId=(.*)\./ ) {
$ftid=$1;
}
elsif ( $desc) {
$desc .= " $continuation_line";
} else {
$desc = $continuation_line;
}
chomp $desc;
}
$self->_pushback($_);
unless( $key ) {
$self->warn("No feature key in putative feature table line: $line");
return;
}
my $out = Bio::SeqIO::FTHelper->new(-verbose => $self->verbose());
$out->key($key);
$out->loc($loc);
if ( $desc && length($desc) ) {
$desc =~ s/\.$//;
push(@{$out->field->{"description"}}, $desc);
}
if ( $ftid ) {
push(@{$out->field->{"FTId"}}, $ftid);
}
return $out;} | sub _write_line_swissprot
{ my ($self,$pre1,$pre2,$line,$length) = @_;
$length || $self->throw( "Miscalled write_line_swissprot 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$sub\n");
for ($i= ($length - length $pre1);$i < $linel;) {
$sub = substr($line,$i,($subl));
$self->_print( "$pre2$sub\n");
$i += $subl;
}} | sub _write_line_swissprot_regex
{ my ($self,$pre1,$pre2,$line,$regex,$length) = @_;
$length || $self->throw( "Miscalled write_line_swissprot without length. Programming error!");
if ( length $pre1 != length $pre2 ) {
$self->warn( "len 1 is ". length ($pre1) . " len 2 is ". length ($pre2) . "\n");
$self->throw( "Programming error - cannot called write_line_swissprot_regex with different length\n pre1 ($pre1) and\n pre2 ($pre2) tags!");
}
my $subl = $length - (length $pre1) -1 ;
my $first_line = 1;
while ($line =~ m/(.{1,$subl})($regex)/g) {
my $s = $1.$2;
$s =~ s/([\w\.])#(\w)/$1 $2/g
if $pre1 eq "RA " or $pre1 eq "KW ";
substr($s, -1, 1, '') if substr($s, -1, 1) eq ' ';
if ($first_line) {
$self->_print( "$pre1$s\n");
$first_line = 0;
} else {
$self->_print( "$pre2$s\n");
}
}} | sub _post_sort
{ my $obj = shift;
if ( @_ ) {
my $value = shift;
$obj->{'_post_sort'} = $value;
}
return $obj->{'_post_sort'};} | sub _show_dna
{ my $obj = shift;
if ( @_ ) {
my $value = shift;
$obj->{'_show_dna'} = $value;
}
return $obj->{'_show_dna'};} | sub _id_generation_func
{ my $obj = shift;
if ( @_ ) {
my $value = shift;
$obj->{'_id_generation_func'} = $value;
}
return $obj->{'_id_generation_func'};} | sub _ac_generation_func
{ my $obj = shift;
if ( @_ ) {
my $value = shift;
$obj->{'_ac_generation_func'} = $value;
}
return $obj->{'_ac_generation_func'};} | sub _sv_generation_func
{ my $obj = shift;
if ( @_ ) {
my $value = shift;
$obj->{'_sv_generation_func'} = $value;
}
return $obj->{'_sv_generation_func'};} | sub _kw_generation_func
{ my $obj = shift;
if ( @_ ) {
my $value = shift;
$obj->{'_kw_generation_func'} = $value;
}
return $obj->{'_kw_generation_func'};
}
1;} | General documentation
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
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/
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Title : _filehandle
Usage : $obj->_filehandle($newval)
Function:
Example :
Returns : value of _filehandle
Args : newvalue (optional)