Bio::LiveSeq::IO Loader
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Summary
Bio::LiveSeq::IO::Loader - Parent Loader for LiveSeq
Package variables
No package variables defined.
Included modules
Bio::LiveSeq::AARange
Bio::LiveSeq::DNA
Bio::LiveSeq::Exon
Bio::LiveSeq::Gene
Bio::LiveSeq::Intron
Bio::LiveSeq::Prim_Transcript
Bio::LiveSeq::Repeat_Region
Bio::LiveSeq::Repeat_Unit
Bio::LiveSeq::Transcript
Bio::LiveSeq::Translation
Bio::Tools::CodonTable
Carp qw ( cluck croak carp )
Synopsis
  #documentation needed
Description
This package holds common methods used by BioPerl and file loaders.
It contains methods to create LiveSeq objects out of entire entries or from a
localized sequence region surrounding a particular gene.
Methods
entry2liveseqDescriptionCode
gene2liveseqDescriptionCode
test_transl
No description
Code
hash2liveseq
No description
Code
hash2gene
No description
Code
rangeofarray
No description
Code
transexonscreation
No description
Code
printswissprotDescriptionCode
printemblDescriptionCode
genesDescriptionCode
swisshash2liveseq
No description
Code
get_swisshash
No description
Code
_findgenefeatures
No description
Code
_checkfeatureproximity
No description
Code
_get_alignment
No description
Code
_common_novelaasequence2gene
No description
Code
Methods description
entry2liveseqcode    nextTop
  Title   : entry2liveseq
Usage : @translationobjects=$loader->entry2liveseq();
: @translationobjects=$loader->entry2liveseq(-getswissprotinfo => 0);
Function: creates LiveSeq objects from an entry previously loaded
Returns : array of references to objects of class Translation
Errorcode 0
Args : optional boolean flag to avoid the retrieval of SwissProt
information for all Transcripts containing SwissProt x-reference
default is 1 (to retrieve those information and create AARange
LiveSeq objects)
Note : this method can get really slow for big entries. The lightweight
gene2liveseq method is recommended
gene2liveseqcodeprevnextTop
  Title   : gene2liveseq
Usage : $gene=$loader->gene2liveseq(-gene_name => "gene name");
: $gene=$loader->gene2liveseq(-gene_name => "gene name",
-flanking => 64);
: $gene=$loader->gene2liveseq(-gene_name => "gene name",
-getswissprotinfo => 0);
: $gene=$loader->gene2liveseq(-position => 4);
Function: creates LiveSeq objects from an entry previously loaded It is a "light weight" creation because it creates a LiveSequence just for the interesting region in an entry (instead than for the total entry, like in entry2liveseq) and for the flanking regions up to 500 nucleotides (default) or up to the specified amount of nucleotides (given as argument) around the Gene. Returns : reference to a Gene object containing possibly alternative Transcripts. Errorcode 0 Args : string containing the gene name as in the EMBL feature qualifier integer (optional) "flanking": amount of flanking bases to be kept boolean (optional) "getswissprotinfo": if set to "0" it will avoid trying to fetch information from a crossreference to a SwissProt entry, avoding the process of creation of AARange objects It is "1" (on) by default Alternative to a gene_name, a position can be given: an integer (1-) containing the position of the desired CDS in the loaded entry
printswissprotcodeprevnextTop
  Title   : printswissprot
Usage : $loader->printswissprot($hashref);
Function: prints out all information loaded from a database entry into the
loader. Mainly used for testing purposes.
Args : a hashref containing the SWISSPROT entry datas
Note : the hashref can be obtained with a call to the method
$loader->get_swisshash() (BioPerl via Bio::DB::EMBL.pm)
that takes as argument a string like "SWISS-PROT:P10275"
printemblcodeprevnextTop
  Title   : printembl
Usage : $loader->printembl();
Function: prints out all information loaded from a database entry into the
loader. Mainly used for testing purposes.
Args : none
genescodeprevnextTop
  Title   : genes
Usage : $loader->genes();
Function: Returns an array of gene_names (strings) contained in the loaded
entry.
Args : none
Methods code
entry2liveseqdescriptionprevnextTop
sub entry2liveseq {
  my ($self, %args) = @_;
  my ($getswissprotinfo)=($args{-getswissprotinfo});
  if (defined($getswissprotinfo)) {
    if (($getswissprotinfo ne 0)&&($getswissprotinfo ne 1)) {
      carp "-getswissprotinfo argument can take only boolean (1 or 0) values. Setting it to 0, i.e. not trying to retrieve SwissProt information....";
      $getswissprotinfo=0;
    }
  } else {
    $getswissprotinfo=1;
  }
  my $hashref=$self->{'hash'};
  unless ($hashref) { return (0); }
  my @translationobjects=$self->hash2liveseq($hashref,$getswissprotinfo);
  my $test_transl=0;
  if ($test_transl) { $self->test_transl($hashref,\@translationobjects);}
  return @translationobjects;
}
gene2liveseqdescriptionprevnextTop
sub gene2liveseq {
  my ($self, %args) = @_;
  my ($gene_name,$flanking,$getswissprotinfo,$cds_position)=($args{-gene_name},$args{-flanking},$args{-getswissprotinfo},$args{-position});
  my $input;
  unless (($gene_name)||($cds_position)) {
    carp "Gene_Name or Position not specified for gene2liveseq loading function";
    return (0);
  }
  if (($gene_name)&&($cds_position)) {
    carp "Gene_Name and Position cannot be given together";
    return (0);
  } elsif ($gene_name) {
    $input=$gene_name;
  } else {
    $input="cds-position:".$cds_position;
  }

  if (defined($getswissprotinfo)) {
    if (($getswissprotinfo ne 0)&&($getswissprotinfo ne 1)) {
      carp "-getswissprotinfo argument can take only boolean (1 or 0) values. Setting it to 0, i.e. not trying to retrieve SwissProt information....";
      $getswissprotinfo=0;
    }
  } else {
    $getswissprotinfo=1;
  }

  if (defined($flanking)) {
    unless ($flanking >= 0) {
      carp "No sense in specifying a number < 0 for flanking regions to be created for gene2liveseq loading function";
      return (0);
    }
  } else {
    $flanking=500; # the default flanking length
} my $hashref=$self->{'hash'}; unless ($hashref) { return (0); } my $gene=$self->hash2gene($hashref,$input,$flanking,$getswissprotinfo); unless ($gene) { # if $gene == 0 it means problems in hash2gene
carp "gene2liveseq produced error"; return (0); } return $gene; } # TODO: update so that it will work even if CDS is not only accepted FEATURE!!
# this method is for now deprecated and not supported
}
test_transldescriptionprevnextTop
sub test_transl {
  my ($self,$entry)=@_;
  my @features=@{$entry->{'Features'}};
  my @translationobjects=@{$_[1]};
  my ($i,$translation);
  my ($obj_transl,$hash_transl);
  my @cds=@{$entry->{'CDS'}};
  foreach $translation (@translationobjects) {
    $obj_transl=$translation->seq;
    $hash_transl=$cds[$i]->{'qualifiers'}->{'translation'};
    #before seq was changed in Translation 1.4# chop $obj_transl; # to remove trailing "*"
unless ($obj_transl eq $hash_transl) { cluck "Serious error: Translation from the Entry does not match Translation from object's seq for CDS at position $i"; carp "\nEntry's transl: ",$hash_transl,"\n"; carp "\nObject's transl: ",$obj_transl,"\n"; exit; } $i++; } } # argument: hashref containing the EMBL entry datas,
# getswissprotinfo boolean flag
# creates the liveseq objects
# returns: an array of Translation object references
}
hash2liveseqdescriptionprevnextTop
sub hash2liveseq {
  my ($self,$entry,$getswissprotinfo)=@_;
  my $i;
  my @transcripts;
  my $dna=Bio::LiveSeq::DNA->new(-seq => $entry->{'Sequence'} );
  $dna->alphabet(lc($entry->{'Molecule'}));
  $dna->display_id($entry->{'ID'});
  $dna->accession_number($entry->{'AccNumber'});
  $dna->desc($entry->{'Description'});
  my @cds=@{$entry->{'CDS'}};
  my ($swissacc,$swisshash); my @swisshashes;
  for $i (0..$#cds) {
    #my @transcript=@{$cds[$i]->{'range'}};
#$transcript=\@transcript;
#push (@transcripts,$transcript);
push (@transcripts,$cds[$i]->{'range'}); if ($getswissprotinfo) { $swissacc=$cds[$i]->{'qualifiers'}->{'db_xref'}; $swisshash=$self->get_swisshash($swissacc); #$self->printswissprot($swisshash); # DEBUG
push (@swisshashes,$swisshash); } } my @translations=($self->transexonscreation($dna,\@transcripts)); my $translation; my $j=0; foreach $translation (@translations) { if ($swisshashes[$j]) { # if not 0
$self->swisshash2liveseq($swisshashes[$j],$translation); } $j++; } return (@translations); } # only features pertaining to a specified gene are created
# only the sequence of the gene and appropriate context flanking regions
# are created as chain
# arguments: hashref, gene_name (OR: cds_position), length_of_flanking_sequences, getswissprotinfo boolean flag
# returns: reference to Gene object
#
# Note: if entry contains just one CDS, all the features get added
# this is useful because often the features in these entries do not
# carry the /gene qualifier
#
# errorcode: 0
}
hash2genedescriptionprevnextTop
sub hash2gene {
  my ($self,$entry,$input,$flanking,$getswissprotinfo)=@_;
  my $entryfeature;
  my $genefeatureshash;

  my @cds=@{$entry->{'CDS'}};

  # checking if a position has been given instead than a gene_name
if (index($input,"cds-position:") == 0 ) { my $cds_position=substr($input,13); # extracting the cds position
if (($cds_position >= 1)&&($cds_position <= scalar(@cds))) { $genefeatureshash=$self->_findgenefeatures($entry,undef,$cds_position,$getswissprotinfo); } } else { $genefeatureshash=$self->_findgenefeatures($entry,$input,undef,$getswissprotinfo); } unless (($genefeatureshash)&&(scalar(@{$genefeatureshash->{'genefeatures'}}))) { # array empty, no gene features found
my @genes=$self->genes($entry); my $cds_number=scalar(@cds); warn "Warning! Not even one genefeature found for /$input/.... The genes present in this entry are:\n\t@genes\n The number of CDS in this entry is:\n\t$cds_number\n"; return(0); } # get max and min, check flankings
my ($min,$max)=$self->rangeofarray(@{$genefeatureshash->{'labels'}}); # gene "boundaries"
my $seqlength=$entry->{'SeqLength'}; my ($mindna,$maxdna); # some flanking region next to the gene "boundaries"
if ($min-$flanking < 1) { $mindna=1; } else { $mindna=$min-$flanking; } if ($max+$flanking > $seqlength) { $maxdna=$seqlength; } else { $maxdna=$max+$flanking; } my $subseq=substr($entry->{'Sequence'},$mindna-1,$maxdna-$mindna+1); # create LiveSeq objects
# create DNA
my $dna=Bio::LiveSeq::DNA->new(-seq => $subseq, -offset => $mindna); $dna->alphabet(lc($entry->{'Molecule'})); $dna->source($entry->{'Organism'}); $dna->display_id($entry->{'ID'}); $dna->accession_number($entry->{'AccNumber'}); $dna->desc($entry->{'Description'}); my @transcripts=@{$genefeatureshash->{'transcripts'}}; # create Translations, Transcripts, Exons out of the CDS
unless (@transcripts) { cluck "no CDS feature found for /$input/...."; return(0); } my @translationobjs=$self->transexonscreation($dna,\@transcripts); my @transcriptobjs; # get the Transcript obj_refs
my $translation; my $j=0; my @ttables=@{$genefeatureshash->{'ttables'}}; my @swisshashes=@{$genefeatureshash->{'swisshashes'}}; foreach $translation (@translationobjs) { push(@transcriptobjs,$translation->get_Transcript); if ($ttables[$j]) { # if not undef
$translation->get_Transcript->translation_table($ttables[$j]); #} else { # DEBUG
# print "\n\t\tno translation table information....\n";
} if ($swisshashes[$j]) { # if not 0
$self->swisshash2liveseq($swisshashes[$j],$translation); } $j++; } my %gene; # this is the hash to store created object references
$gene{DNA}=$dna; $gene{Transcripts}=\@transcriptobjs; $gene{Translations}=\@translationobjs; my @exonobjs; my @intronobjs; my @repeatunitobjs; my @repeatregionobjs; my @primtranscriptobjs; my ($object,$range,$start,$end,$strand); my @exons=@{$genefeatureshash->{'exons'}}; my @exondescs=@{$genefeatureshash->{'exondescs'}}; if (@exons) { my $exoncount = 0; foreach $range (@exons) { ($start,$end,$strand)=@{$range}; $object = Bio::LiveSeq::Exon->new(-seq=>$dna,-start=>$start,-end=>$end,-strand=>$strand); if ($object != -1) { $object->desc($exondescs[$exoncount]) if defined $exondescs[$exoncount]; $exoncount++; push (@exonobjs,$object); } else { $exoncount++; } } $gene{Exons}=\@exonobjs; } my @introns=@{$genefeatureshash->{'introns'}}; my @introndescs=@{$genefeatureshash->{'introndescs'}}; if (@introns) { my $introncount = 0; foreach $range (@introns) { ($start,$end,$strand)=@{$range}; $object=Bio::LiveSeq::Intron->new(-seq=>$dna,-start=>$start,-end=>$end,-strand=>$strand); if ($object != -1) { $object->desc($introndescs[$introncount]); $introncount++; push (@intronobjs,$object); } else { $introncount++; } } $gene{Introns}=\@intronobjs; } my @prim_transcripts=@{$genefeatureshash->{'prim_transcripts'}}; if (@prim_transcripts) { foreach $range (@prim_transcripts) { ($start,$end,$strand)=@{$range}; $object=Bio::LiveSeq::Prim_Transcript->new(-seq=>$dna,-start=>$start,-end=>$end,-strand=>$strand); if ($object != -1) { push (@primtranscriptobjs,$object); } } $gene{Prim_Transcripts}=\@primtranscriptobjs; } my @repeat_regions=@{$genefeatureshash->{'repeat_regions'}}; my @repeat_regions_family=@{$genefeatureshash->{'repeat_regions_family'}}; if (@repeat_regions) { my $k=0; foreach $range (@repeat_regions) { ($start,$end,$strand)=@{$range}; $object=Bio::LiveSeq::Repeat_Region->new(-seq=>$dna,-start=>$start,-end=>$end,-strand=>$strand); if ($object != -1) { $object->desc($repeat_regions_family[$k]); $k++; push (@repeatregionobjs,$object); } else { $k++; } } $gene{Repeat_Regions}=\@repeatregionobjs; } my @repeat_units=@{$genefeatureshash->{'repeat_units'}}; my @repeat_units_family=@{$genefeatureshash->{'repeat_units_family'}}; if (@repeat_units) { my $k=0; foreach $range (@repeat_units) { ($start,$end,$strand)=@{$range}; $object=Bio::LiveSeq::Repeat_Unit->new(-seq=>$dna,-start=>$start,-end=>$end,-strand=>$strand); if ($object != -1) { $object->desc($repeat_units_family[$k]); $k++; push (@repeatunitobjs,$object); } else { $k++; } } $gene{Repeat_Units}=\@repeatunitobjs; } # create the Gene
my $gene_name=$genefeatureshash->{'gene_name'}; # either a name or a cdspos
return (Bio::LiveSeq::Gene->new(-name=>$gene_name,-features=>\%gene, -upbound=>$min,-downbound=>$max)); } # maybe this function will be moved to general utility package
# argument: array of numbers
# returns: (min,max) numbers in the array
}
rangeofarraydescriptionprevnextTop
sub rangeofarray {
  my $self=shift;
  my @array=@_;
  #print "\n-=-=-=-=-=-=-=-=-=-=array: @array\n";
my ($max,$min,$element); $min=$max=shift(@array); foreach $element (@array) { $element = 0 unless defined $element; if ($element < $min) { $min=$element; } if ($element > $max) { $max=$element; } } #print "\n-=-=-=-=-=-=-=-=-=-=min: $min\tmax: $max\n";
return ($min,$max); } # argument: reference to DNA object, reference to array of transcripts
# returns: an array of Translation object references
}
transexonscreationdescriptionprevnextTop
sub transexonscreation {
  my $self=shift;
  my $dna=$_[0];
  my @transcripts=@{$_[1]};

  my (@transexons,$start,$end,$strand,$exonref,$exonobj,$transcript,$transcriptobj);
  my $translationobj;
  my @translationobjects;
  foreach $transcript (@transcripts) {
    foreach $exonref (@{$transcript}) {
      ($start,$end,$strand)=@{$exonref};
      #print "Creating Exon: start $start end $end strand $strand\n";
$exonobj=Bio::LiveSeq::Exon->new(-seq=>$dna,-start=>$start,-end=>$end,-strand=>$strand); #push (@exonobjects,$exonobj);
push (@transexons,$exonobj); } $transcriptobj=Bio::LiveSeq::Transcript->new(-exons =>\@ transexons ); if ($transcriptobj != -1) { $translationobj=Bio::LiveSeq::Translation->new(-transcript=>$transcriptobj); @transexons=(); # cleans it
#push (@transcriptobjects,$transcriptobj);
push (@translationobjects,$translationobj); } } return (@translationobjects); } #sub printgene {
# deleted. Some functionality placed in Gene->printfeaturesnum
}
printswissprotdescriptionprevnextTop
sub printswissprot {
  my ($self,$entry)=@_;
  unless ($entry) {
    return;
  }
  printf "ID: %s\n",
      $entry->{'ID'};
  printf "ACC: %s\n",
      $entry->{'AccNumber'};
  printf "GENE: %s\n",
      $entry->{'Gene'};
  printf "DES: %s\n",
      $entry->{'Description'};
  printf "ORG: %s\n",
      $entry->{'Organism'};
  printf "SEQLN: %s\n",
      $entry->{'SeqLength'};
  printf "SEQ: %s\n",
      substr($entry->{'Sequence'},0,64);
  if ($entry->{'Features'}) {
    my @features=@{$entry->{'Features'}};
    my $i;
    for $i (0..$#features) {
      print "|",$features[$i]->{'name'},"|";
      print " at ",$features[$i]->{'location'},": ";
      print "",$features[$i]->{'desc'},"\n";
    }
  }
}
printembldescriptionprevnextTop
sub printembl {
  my ($self,$entry)=@_;
  unless ($entry) {
    $entry=$self->{'hash'};
  }
  my ($i,$featurename);
  printf "ID: %s\n",
      $entry->{'ID'};
  printf "ACC: %s\n",
      $entry->{'AccNumber'};
  printf "MOL: %s\n",
      $entry->{'Molecule'};
  printf "DIV: %s\n",
      $entry->{'Division'};
  printf "DES: %s\n",
      $entry->{'Description'};
  printf "ORG: %s\n",
      $entry->{'Organism'};
  printf "SEQLN: %s\n",
      $entry->{'SeqLength'};
  printf "SEQ: %s\n",
      substr($entry->{'Sequence'},0,64);
  my @features=@{$entry->{'Features'}};
  my @cds=@{$entry->{'CDS'}};
  print "\nFEATURES\nNumber of CDS: ",scalar(@cds)," (out of ",$entry->{'FeaturesNumber'}, " total features)\n";
  my ($exonref,$transcript);
  my ($qualifiernumber,$qualifiers,$key);
  my ($start,$end,$strand);
  my $j=0;
  for $i (0..$#features) {
    $featurename=$features[$i]->{'name'};
    if ($featurename eq "CDS") {
      print "|CDS| number $j at feature position: $i\n";
      #print $features[$i]->{'location'},"\n";
$transcript=$features[$i]->{'range'}; foreach $exonref (@{$transcript}) { ($start,$end,$strand)=@{$exonref}; print "\tExon: start $start end $end strand $strand\n"; } $j++; } else { print "|$featurename| at feature position: $i\n"; print "\trange: "; print join("\t",@{$features[$i]->{'range'}}),"\n"; #print $features[$i]->{'location'},"\n";
} $qualifiernumber=$features[$i]->{'qual_number'}; $qualifiers=$features[$i]->{'qualifiers'}; # hash
foreach $key (keys (%{$qualifiers})) { print "\t\t",$key,": "; print $qualifiers->{$key},"\n"; } }
}
genesdescriptionprevnextTop
sub genes {
  my ($self,$entry)=@_;
  unless ($entry) {
    $entry=$self->{'hash'};
  }
  my @entryfeatures=@{$entry->{'Features'}};
  my ($genename,$genenames,$entryfeature);
  for $entryfeature (@entryfeatures) {
    $genename=$entryfeature->{'qualifiers'}->{'gene'};
    if ($genename) {
      if (index($genenames,$genename) == -1) { # if name is new
$genenames .= $genename . " "; # add the name
} } } return (split(/ /,$genenames)); # assumes no space inbetween each genename
} # arguments: swisshash, translation objref
# adds information to the Translation, creates AARange objects, sets the
# aa_range attribute on the Translation, pointing to those objects
}
swisshash2liveseqdescriptionprevnextTop
sub swisshash2liveseq {
  my ($self,$entry,$translation)=@_;
  my $translength=$translation->length;
  $translation->desc($translation->desc . $entry->{'Description'});
  $translation->display_id("SWISSPROT:" . $entry->{'ID'});
  $translation->accession_number("SWISSPROT:" . $entry->{'AccNumber'});
  $translation->name($entry->{'Gene'});
  $translation->source($entry->{'Organism'});
  my @aarangeobjects;
  my ($start,$end,$aarangeobj,$feature);
  my @features; my @newfeatures;
  if ($entry->{'Features'}) {
    @features=@{$entry->{'Features'}};
  }
  my $cleavedmet=0;
  # check for cleaved Met
foreach $feature (@features) { if (($feature->{'name'} eq "INIT_MET")&&($feature->{'location'} eq "0 0")) { $cleavedmet=1; $translation->{'offset'}="1"; # from swissprot to liveseq protein sequence
} else { push(@newfeatures,$feature); } } my $swissseq=$entry->{'Sequence'}; my $liveseqtransl=$translation->seq; chop $liveseqtransl; # to take away the trailing STOP "*"
my $translated=substr($liveseqtransl,$cleavedmet); my ($liveseq_aa,$swiss_aa,$codes_aa)=$self->_get_alignment($translated,$swissseq); # alignment after cleavage of possible initial met
if ((index($liveseq_aa,"-") != -1)||(index($swiss_aa,"-") != -1)) { # there are gaps, how to proceed?
print "LIVE-SEQ=\'$liveseq_aa\'\nIDENTITY=\'$codes_aa\'\nSWS-PROT=\'$swiss_aa\'\n"; carp "Nucleotides translation and SwissProt translation are different in size, cannot attach the SwissSequence to the EMBL one, cannot add any AminoAcidRange object/Domain information!"; return; } #my $i=0; # debug
@features=@newfeatures; foreach $feature (@features) { #print "Processing SwissProtFeature: $i\n"; # debug
($start,$end)=split(/ /,$feature->{'location'}); # Note: cleavedmet is taken in account for updating numbering
$aarangeobj=Bio::LiveSeq::AARange->new(-start => $start+$cleavedmet, -end => $end+$cleavedmet, -name => $feature->{'name'}, -description => $feature->{'description'}, -translation => $translation, -translength => $translength); if ($aarangeobj != -1) { push(@aarangeobjects,$aarangeobj); } # $i++; # debug
} $translation->{'aa_ranges'}=\@aarangeobjects; } # if there is no SRS support, the default will be to return 0
# i.e. this function is overridden in SRS package
}
get_swisshashdescriptionprevnextTop
sub get_swisshash {
  return (0);
}

# Args: $entry hashref, gene_name OR cds_position (undef is used to
# choose between the two), getswissprotinfo boolean flag
# Returns: an hash holding various arrayref used in the hash2gene method
# Function: examines the nucleotide entry, identifying features belonging
# to the gene (defined either by its name or by the position of its CDS in
# the entry)
}
_findgenefeaturesdescriptionprevnextTop
sub _findgenefeatures {
  my ($self,$entry,$gene_name,$cds_position,$getswissprotinfo)=@_;

  my @entryfeatures=@{$entry->{'Features'}};
  my @exons; my @introns; my @prim_transcripts; my @transcripts;
  my @repeat_units; my @repeat_regions;
  my @repeat_units_family; my @repeat_regions_family; my $rpt_family;
  my $entryfeature; my @genefeatures;
  my $desc; my @exondescs; my @introndescs;

  # for swissprot xreference
my ($swissacc,$swisshash); my @swisshashes; # for translation_tables
my @ttables; # to create labels
my ($name,$exon); my @range; my @cdsexons; my @labels; # maybe here also could be added special case when there is no CDS feature
# in the entry (e.g. tRNA entry -> TOCHECK).
# let's deal with the special case in which there is just one gene per entry
# usually without /gene qualifier
my @cds=@{$entry->{'CDS'}}; my $skipgenematch=0; if (scalar(@cds) == 1) { #carp "Note: only one CDS in this entry. Treating all features found in entry as Gene features.";
$skipgenematch=1; } my ($cds_begin,$cds_end,$proximity); if ($cds_position) { # if a position has been requested
my @cds_exons=@{$cds[$cds_position-1]->{'range'}}; ($cds_begin,$cds_end)=($cds_exons[0]->[0],$cds_exons[-1]->[1]); # begin and end of CDS
$gene_name=$cds[$cds_position-1]->{'qualifiers'}->{'gene'}; # DEBUG
unless ($skipgenematch) { carp "--DEBUG-- cdsbegin $cds_begin cdsend $cds_end--------"; } $proximity=100; # proximity CONSTANT to decide whether a feature "belongs" to the CDS
} for $entryfeature (@entryfeatures) { # get only features for the desired gene
if (($skipgenematch)||(($cds_position)&&($self->_checkfeatureproximity($entryfeature->{'range'},$cds_begin,$cds_end,$proximity)))||(!($cds_position)&&($entryfeature->{'qualifiers'}->{'gene'} eq "$gene_name"))) { push(@genefeatures,$entryfeature); my @range=@{$entryfeature->{'range'}}; $name=$entryfeature->{'name'}; my %qualifierhash=%{$entryfeature->{'qualifiers'}}; if ($name eq "CDS") { # that has range containing array of exons
# swissprot crossindexing (if without SRS support it will fill array
# with zeros and do nothing
if ($getswissprotinfo) { $swissacc=$entryfeature->{'qualifiers'}->{'db_xref'}; $swisshash=$self->get_swisshash($swissacc); #$self->printswissprot($swisshash); # DEBUG
push (@swisshashes,$swisshash); } push (@ttables,$entryfeature->{'qualifiers'}->{'transl_table'}); # undef if not specified
# create labels array
for $exon (@range) { push(@labels,$exon->[0],$exon->[1]); # start and end of every exon of the CDS
} push (@transcripts,$entryfeature->{'range'}); } else { # "simplifying" the joinedlocation features. I.e. changing them from
# multijoined ones to simple plain start-end features, taking only
# the start of the first "exon" and the end of the last "exon" as
# start and end of the entire feature
if ($entryfeature->{'locationtype'} && $entryfeature->{'locationtype'} eq "joined") { # joined location
@range=($range[0]->[0],$range[-1]->[1]); } push(@labels,$range[0],$range[1]); # start and end of every feature
if ($name eq "exon") { $desc=$entryfeature->{'qualifiers'}->{'number'}; if ($entryfeature->{'qualifiers'}->{'note'}) { if ($desc) { $desc .= "|" . $entryfeature->{'qualifiers'}->{'note'}; } else { $desc = $entryfeature->{'qualifiers'}->{'note'}; } } push (@exondescs,$desc || "unknown"); push(@exons,\@range); } if ($name eq "intron") { $desc=$entryfeature->{'qualifiers'}->{'number'}; if ($desc) { $desc .= "|" . $entryfeature->{'qualifiers'}->{'note'}; } else { $desc = $entryfeature->{'qualifiers'}->{'note'}; } push (@introndescs,$desc || "unknown"); push(@introns,\@range); } if (($name eq "prim_transcript")||($name eq "mRNA")) { push(@prim_transcripts,\@range); } if ($name eq "repeat_unit") { push(@repeat_units,\@range); $rpt_family=$entryfeature->{'qualifiers'}->{'rpt_family'}; push (@repeat_units_family,$rpt_family || "unknown"); } if ($name eq "repeat_region") { push(@repeat_regions,\@range); $rpt_family=$entryfeature->{'qualifiers'}->{'rpt_family'}; push (@repeat_regions_family,$rpt_family || "unknown"); } } } } unless ($gene_name) { $gene_name="cds-position:".$cds_position; } my %genefeatureshash; $genefeatureshash{gene_name}=$gene_name; $genefeatureshash{genefeatures}=\@genefeatures; $genefeatureshash{labels}=\@labels; $genefeatureshash{ttables}=\@ttables; $genefeatureshash{swisshashes}=\@swisshashes; $genefeatureshash{transcripts}=\@transcripts; $genefeatureshash{exons}=\@exons; $genefeatureshash{exondescs}=\@exondescs; $genefeatureshash{introns}=\@introns; $genefeatureshash{introndescs}=\@introndescs; $genefeatureshash{prim_transcripts}=\@prim_transcripts; $genefeatureshash{repeat_units}=\@repeat_units; $genefeatureshash{repeat_regions}=\@repeat_regions; $genefeatureshash{repeat_units_family}=\@repeat_units_family; $genefeatureshash{repeat_regions_family}=\@repeat_regions_family; return (\%genefeatureshash); } # used by _findgenefeatures, when a CDS at a certain position is requested,
# to retrieve only features quite close to the wanted CDS.
# Args: range hashref, begin and end positions of the CDS, $proximity
# $proximity holds the maximum distance between the extremes of the CDS
# and of the feature under exam.
# Returns: boolean
}
_checkfeatureproximitydescriptionprevnextTop
sub _checkfeatureproximity {
  my ($self,$range,$cds_begin,$cds_end,$proximity)=@_;
  my @range=@{$range};
  my ($begin,$end,$strand);
  if (ref($range[0]) eq "ARRAY") { # like in CDS, whose range equivals to exons
($begin,$end,$strand)=($range[0]->[0],$range[-1]->[1],$range[0]->[2]); } else { ($begin,$end,$strand)=@range; } if ($cds_begin > $cds_end) { # i.e. reverse strand CDS
($cds_begin,$cds_end)=($cds_end,$cds_begin); # swap boundaries
} if ($strand == -1) { # reverse strand
($begin,$end)=($end,$begin); # swap boundaries
} if (($cds_begin-$end)>$proximity) { carp "--DEBUG-- feature rejected: begin $begin end $end -------"; return (0); } if (($begin-$cds_end)>$proximity) { carp "--DEBUG-- feature rejected: begin $begin end $end -------"; return (0); } carp "--DEBUG-- feature accepted: begin $begin end $end -------"; return (1); # otherwise ok, feature considered next to CDS
} # function that calls the external program "align" (on the fasta2 package)
# to create an alignment between two sequences, returning the aligned
# strings and the codes for the identity (:: ::::)
}
_get_alignmentdescriptionprevnextTop
sub _get_alignment {
  my ($self,$seq1,$seq2)=@_;
  my $fastafile1="/tmp/tmpfastafile1";
  my $fastafile2="/tmp/tmpfastafile2";
  my $grepcut='egrep -v "[[:digit:]]|^ *$|sequences" | cut -c8-'; # grep/cut
my $alignprogram="/usr/local/etc/bioinfo/fasta2/align -s /usr/local/etc/bioinfo/fasta2/idnaa.mat $fastafile1 $fastafile2 2>/dev/null | $grepcut"; # ALIGN
open my $TMPFASTAFILE1,">$fastafile1" || croak "Cannot write into $fastafile1 for aa alignment"; open my $TMPFASTAFILE2,">$fastafile2" || croak "Cannot write into $fastafile1 for aa alignment"; print $TMPFASTAFILE1 ">firstseq\n$seq1\n"; print $TMPFASTAFILE2 ">secondseq\n$seq2\n"; close $TMPFASTAFILE1; close $TMPFASTAFILE2; my $alignment=`$alignprogram`; my @alignlines=split(/\n/,$alignment); my ($linecount,$seq1_aligned,$seq2_aligned,$codes); for ($linecount=0; $linecount < @alignlines; $linecount+=3) { $seq1_aligned .= $alignlines[$linecount]; $codes .= $alignlines[$linecount+1]; $seq2_aligned .= $alignlines[$linecount+2]; } return ($seq1_aligned,$seq2_aligned,$codes); } # common part of the function to create a novel liveseq gene structure
# from an amino acid sequence, using codon usage frequencies
# args: codon_usage_array transltableid aasequence gene_name
}
_common_novelaasequence2genedescriptionprevnextTop
sub _common_novelaasequence2gene {
  my ($species_codon_usage,$ttabid,$aasequence,$gene_name)=@_;
  my @species_codon_usage=@{$species_codon_usage};
  my @codon_usage_label= 
      qw (cga cgc cgg cgt aga agg cta ctc ctg ctt tta ttg tca tcc tcg
      tct agc agt aca acc acg act cca ccc ccg cct gca gcc gcg gct gga
      ggc ggg ggt gta gtc gtg gtt aaa aag aac aat caa cag cac cat gaa
      gag gac gat tac tat tgc tgt ttc ttt ata atc att atg tgg taa tag
      tga);
  my ($i,$j);
  my %codon_usage_value;
  my $aa_codon_total;
  for ($i=0;$i<64;$i++) {
    $codon_usage_value{$codon_usage_label[$i]}=$species_codon_usage[$i];
  }

  my $CodonTable  = Bio::Tools::CodonTable->new ( -id => $ttabid );
  my @aminoacids = split(//,uc($aasequence));
  my @alt_codons; my ($relativeusage,$dnasequence,$chosen_codon,$dice,$partial,$thiscodon);
  for $i (@aminoacids) {
    @alt_codons = $CodonTable->revtranslate($i);
    unless (@alt_codons) {
      carp "No reverse translation possible for aminoacid\' $i\'";
      $dnasequence .= "???";
    } else {
      $aa_codon_total=0;
      for $j (@alt_codons) {
	$aa_codon_total+=$codon_usage_value{$j};
      }
      # print "aminoacid $i, codonchoice: "; # verbose
#$partial=0;
#for $j (@alt_codons) {
#printf "%s %.2f ",$j,$partial+$codon_usage_value{$j}/$aa_codon_total;
#$partial+=($codon_usage_value{$j}/$aa_codon_total);
#}
#print "\n";
$dice=rand(1); #print "roulette: $dice\n"; # verbose
$partial=0; $chosen_codon=""; CODONCHOICE: for $j (0..@alt_codons) { # last one not accounted
$thiscodon=$alt_codons[$j]; $relativeusage=($codon_usage_value{$thiscodon}/$aa_codon_total);
if ($dice < $relativeusage+$partial) { $chosen_codon=$thiscodon; last CODONCHOICE; } else { $partial += $relativeusage; } } unless ($chosen_codon) { $chosen_codon = $alt_codons[-1]; # the last one
} # print ".....adding $chosen_codon\n"; # verbose
$dnasequence .= $chosen_codon; } } my $dna = Bio::LiveSeq::DNA->new(-seq => $dnasequence); my $min=1; my $max=length($dnasequence); my $exon = Bio::LiveSeq::Exon->new(-seq => $dna, -start => $min, -end => $max, -strand => 1); my @exons=($exon); my $transcript = Bio::LiveSeq::Transcript->new(-exons =>\@ exons); $transcript->translation_table($ttabid); my @transcripts=($transcript); my $translation = Bio::LiveSeq::Translation->new(-transcript => $transcript); my @translations=($translation); my %features=(DNA => $dna, Transcripts =>\@ transcripts, Translations =>\@ translations); my $gene = Bio::LiveSeq::Gene->new(-name => $gene_name, -features =>\% features, -upbound => $min, -downbound => $max); # creation of gene
unless ($gene) { # if $gene == 0 it means problems in hash2gene
carp "Error in Gene creation phase"; return (0); } return $gene; } 1;
}
General documentation
AUTHOR - Joseph A.L. InsanaTop
Email: Insana@ebi.ac.uk, jinsana@gmx.net
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
novelaasequence2geneTop
  Title   : novelaasequence2gene
Usage : $gene=$loader->novelaasequence2gene(-aasequence => "MGLAAPTRS*");
: $gene=$loader->novelaasequence2gene(-aasequence => "MGLAAPTRS*");
-taxon => 9606,
-gene_name => "tyr-kinase");
Function: creates LiveSeq objects from a novel amino acid sequence, using codon usage database to choose codons according to relative frequencies. If a taxon ID is not specified, the default is to use the human one (taxonomy ID 9606). Returns : reference to a Gene object containing references to LiveSeq objects Errorcode 0 Args : string containing an amino acid sequence integer (optional) with a taxonomy ID string specifying a gene name