# fpc.pm,v 1.2.2.1 2005/10/09 15:16:27 jason Exp
#
# BioPerl module for Bio::MapIO::fpc
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Gaurav Gupta <gaurav@genome.arizona.edu>
#
# Copyright AGCoL
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::MapIO::fpc - A FPC Map reader
=head1 SYNOPSIS
# do not use this object directly it is accessed through the Bio::MapIO system
use Bio::MapIO;
-format : specifies the format of the file format is "fpc",
-file : specifies the name of the .fpc file
-readcor : boolean argument, indicating if .cor is to be read
or not. It looks for the .cor file in the same path
as .fpc file.
0 : doesn't read .cor file
1 : reads the .cor file
[default 0]
-verbose : indicates the process of loading of fpc file
my $mapio = Bio::MapIO->new(-format => "fpc",
-file => "rice.fpc",
-readcor => 0,
-verbose => 0);
my $map = $mapio->next_map();
foreach my $marker ( $map->each_markerid() ) {
# loop through the markers associated with the map
# likewise for contigs, clones, etc.
}
=head1 DESCRIPTION
This object contains code for parsing and processing FPC files and creating
L<Bio::Map::Physical> object from it.
For faster access and better optimization, the data is stored internally in
hashes. The corresponding objects are created on request.
We handle reading of the FPC ourselves, since MapIO module of Bioperl adds
too much overhead.
=cut
# Let the code begin...
package Bio::MapIO::fpc;
use strict;
use POSIX;
use Bio::Map::Physical;
use Bio::Map::Clone;
use Bio::Map::Contig;
use Bio::Map::FPCMarker;
use Bio::Range;
use base qw(Bio::MapIO);
my $_readcor;
=head1 Initializer
=head2 _initialize
Title : _initialize
Usage : called implicitly
Function: calls the SUPER::_initialize
Returns : nothing
Args : species, readcor
=cut
sub _initialize{
my ($self,@args) = @_;
my $species;
$self->SUPER::_initialize(@args);
($species,$_readcor) = $self->_rearrange([qw(SPECIES READCOR)], @args);
$_readcor = 0 unless (defined($_readcor));
}
=head1 Access Methods
These methods let you get and set the member variables
=head2 next_map
Title : next_map
Usage : my $fpcmap = $mapio->next_map();
Function: gets the fpcmap from MapIO
Returns : object of type L<Bio::Map::MapI>
Args : none
=cut
sub next_map{
my ($self) = @_;
my $line;
my ($name,$fpcver,$moddate,$moduser,$contigcnt,$clonecnt,$markerscnt,
$bandcnt,$marker,$seqclone);
my ($corfile,$corindex,$BUFFER);
my @cordata;
my %fpcmarker;
my ($contig, $contigNumber);
my $curClone = 0;
my $curMarker = 0;
my $curContig = 0;
my %_clones;
my %_markers;
my %_contigs;
my $ctgzeropos = 1;
my $map = Bio::Map::Physical->new('-units' => 'CB',
'-type' => 'physical');
my $filename = $self->file();
my $fh = $self->{'_filehandle'};
if (defined($_readcor)) {
$map->core_exists($_readcor);
}
else {
$map->core_exists(0);
}
if ($map->core_exists()) {
$corfile = substr($filename,0,length($filename)-3)."cor";
if (open my $CORE, '<', $corfile) {
while( read($CORE, $BUFFER, 2) ) {
push @cordata, unpack('n*', $BUFFER);
}
}
else {
$map->core_exists(0);
}
}
## Read in the header
while (defined($line = <$fh>)) {
chomp($line);
if ($line =~ m{^//\s+fpc\s+project\s+(.+)}) { $map->name($1); }
if ($line =~ m{^//\s+([\d.]+)}) {
my $version = $1;
$version =~ /((\d+)\.(\d+))(.*)/;
$map->version($1);
if ($line =~ /User:\s+(.+)/) { $map->modification_user($1); }
}
if ($line =~ m{^//\s+Framework\s+(\w+)\s+(\w+)\s+([-\w]+)\s+(\w+)\s+(\w+)\s+(.+)$})
{
$map->group_type($3) if ($2 eq "Label");
$map->group_abbr($5) if ($4 eq "Abbrev");
}
last unless ($line =~ m{^//});
}
if (!defined($map->group_type()) || !defined($map->group_abbr()) ) {
$map->group_type("Chromosome");
$map->group_abbr("Chr");
}
$_contigs{0}{'range'}{'end'} = 0;
$_contigs{0}{'range'}{'start'} = 0;
## Read in the clone data
while (defined($line = <$fh>)) {
$marker = 0;
$contig = 0;
$seqclone = 0;
$contigNumber = 0;
my ($type,$name);
my (@amatch,@pmatch,@ematch);
my $bandsread = 0;
last if ($line =~ /^Markerdata/);
$line =~ /^(\w+)\s+:\s+"(.+)"/;
## these will be set if we did find the clone line
($type, $name) = ($1, $2);
if ($name =~ /sd1/) {
$seqclone = 1;
}
$_clones{$name}{'type'} = $type;
$_clones{$name}{'contig'} = 0;
$_contigs{'0'}{'clones'}{$name} = 0;
my $temp;
## Loop through the following lines, getting attributes for clone
while (defined($line = <$fh>) && $line !~ /^\s*\n$/) {
if ($line =~ /^Map "ctg(\d+)" Ends (Left|Right) ([-\d]+)/) {
$_clones{$name}{'contig'} = $1;
$_contigs{$1}{'clones'}{$name} = 0;
delete($_contigs{'0'}{'clones'}{$name});
$temp = $3;
$contigNumber = $1;
$line = <$fh>;
$line =~ /^Map "ctg(\d+)" Ends (Left|Right) ([\d]+)/;
$_clones{$name}{'range'}{'start'} = $temp;
$_contigs{$contigNumber}{'range'}{'start'} = $temp
if (!exists($_contigs{$contigNumber}{'range'}{'start'})
|| $_contigs{$contigNumber}{'range'}{'start'}
> $temp );
$_clones{$name}{'range'}{'end'} = $3;
$_contigs{$contigNumber}{'range'}{'end'} = $3
if (!exists($_contigs{$contigNumber}{'range'}{'end'})
|| $_contigs{$contigNumber}{'range'}{'end'} < $3 );
}
elsif ($line =~ /^([a-zA-Z]+)_match_to_\w+\s+"(.+)"/) {
my $matchtype = "match" . lc(substr($1, 0, 1));
$_clones{$name}{$matchtype}{$2} = 0;
}
elsif ($line =~ /^Positive_(\w+)\s+"(.+)"/) {
$_clones{$name}{'markers'}{$2} = 0;
$_markers{$2}{'clones'}{$name} = 0;
$_markers{$2}{'type'} = $1;
$_markers{$2}{'contigs'}{$contigNumber} = 0;
$_contigs{$contigNumber}{'markers'}{$2} = 0;
}
elsif ($line =~ /^Bands\s+(\d+)\s+(\d+)/ && !$bandsread) {
my $i = 0;
my @numbands;
$bandsread = 1;
if ($map->core_exists()) {
while($i<$2){
push(@numbands,$cordata[($1-1)+$i]);
$i++;
}
$_clones{$name}{'bands'} = \@numbands;
}
else {
push(@numbands,$1,$2);
$_clones{$name}{'bands'} = \@numbands;
}
if (exists($_contigs{0}{'clones'}{$name})) {
$_clones{$name}{'range'}{'start'} = $ctgzeropos;
$_clones{$name}{'range'}{'end'} = $ctgzeropos + $2;
$_contigs{0}{'range'}{'end'} = $ctgzeropos + $2;
$ctgzeropos += $2;
}
}
elsif ($line =~ /^Gel_number\s+(.+)/) {
$_clones{$name}{'gel'} = $1;
}
elsif ($line =~ /^Remark\s+"(.+)"/) {
$_clones{$name}{'remark'} .= $1;
$_clones{$name}{'remark'} .= "\n";
if($seqclone == 1 ) {
if( $1 =~ /\,\s+Chr(\d+)\s+/){
$_clones{$name}{'group'} = $1;
}
}
}
elsif ($line =~ /^Fp_number\s+"(.+)"/) {
$_clones{$name}{'fp_number'} = $1;
}
elsif ($line =~ /^Shotgun\s+(\w+)\s+(\w+)/) {
$_clones{$name}{'sequence_type'} = $1;
$_clones{$name}{'sequence_status'} = $2;
}
elsif ($line =~ /^Fpc_remark\s+"(.+)"/) {
$_clones{$name}{'fpc_remark'} .= $1;
$_clones{$name}{'fpc_remark'} .= "\n";
}
}
$curClone++;
print "Adding clone $curClone...\n\r"
if ($self->verbose() && $curClone % 1000 == 0);
}
$map->_setCloneRef(\%_clones);
$line = <$fh>;
while (defined($line = <$fh>) && $line !~ /Contigdata/) {
my ($type,$name);
last if ($line !~ /^Marker_(\w+)\s+:\s+"(.+)"/);
($type, $name) = ($1, $2);
$_markers{$name}{'type'} = $type;
$_markers{$name}{'group'} = 0;
$_markers{$name}{'global'} = 0;
$_markers{$name}{'anchor'} = 0;
while (defined($line = <$fh>) && $line !~ /^\s*\n$/) {
if ($line =~ /^Global_position\s+([\d.]+)\s*(Frame)?/) {
my $position = $1 - floor($1/1000)*1000;
$position = sprintf("%.2f",$position);
$_markers{$name}{'global'} = $position;
$_markers{$name}{'group'} = floor($1/1000);
$_markers{$name}{'anchor'} = 1;
if(defined($2)) {
$_markers{$name}{'framework'} = 1;
}
else {
$_markers{$name}{'framework'} = 0;
}
}
elsif ($line =~ /^Anchor_bin\s+"([\w\d.]+)"/) {
my $grpmatch = $1;
my $grptype = $map->group_type();
$grpmatch =~ /(\d+|\w)(.*)/;
my ($group,$subgroup);
$group = $1;
$subgroup = $2;
$subgroup = substr($subgroup,1) if ($subgroup =~ /^\./);
$_markers{$name}{'group'} = $group;
$_markers{$name}{'subgroup'} = $subgroup;
}
elsif ($line =~ /^Anchor_pos\s+([\d.]+)\s+(F|P)?/){
$_markers{$name}{'global'} = $1;
$_markers{$name}{'anchor'} = 1;
if ($2 eq 'F') {
$_markers{$name}{'framework'} = 1;
}
else {
$_markers{$name}{'framework'} = 0;
}
}
elsif ($line =~ /^anchor$/) {
$_markers{$name}{'anchor'} = 1;
}
elsif ($line =~ /^Remark\s+"(.+)"/) {
$_markers{$name}{'remark'} .= $1;
$_markers{$name}{'remark'} .= "\n";
}
}
$curMarker++;
print "Adding Marker $curMarker...\n"
if ($self->verbose() && $curMarker % 1000 == 0);
}
$map->_setMarkerRef(\%_markers);
my $ctgname;
my $grpabbr = $map->group_abbr();
my $chr_remark;
$_contigs{0}{'group'} = 0;
while (defined($line = <$fh>)) {
if ($line =~ /^Ctg(\d+)/) {
$ctgname = $1;
$_contigs{$ctgname}{'group'} = 0;
$_contigs{$ctgname}{'anchor'} = 0;
$_contigs{$ctgname}{'position'} = 0;
if ($line =~ /#\w*(.*)\w*$/) {
$_contigs{$ctgname}{'remark'} = $1;
if ($line =~ /#\s+Chr(\d+)\s+/) {
$_contigs{$ctgname}{'group'} = $1;
$_contigs{$ctgname}{'anchor'} = 1;
}
}
}
elsif ($line =~ /^Chr_remark\s+"(-|\+|Chr(\d+))\s+(.+)"$/) {
$_contigs{$ctgname}{'anchor'} = 1;
$_contigs{$ctgname}{'chr_remark'} = $3 if(defined($3));
if (defined($2)) {
$_contigs{$ctgname}{'group'} = $2;
}
else {
$_contigs{$ctgname}{'group'} = "?";
}
}
elsif ($line =~ /^User_remark\s+"(.+)"/) {
$_contigs{$ctgname}{'usr_remark'} = $1;
}
elsif ($line =~ /^Trace_remark\s+"(.+)"/) {
$_contigs{$ctgname}{'trace_remark'} = $1;
}
elsif ($grpabbr && $line =~ /^Chr_remark\s+"(\W|$grpabbr((\d+)|(\w+)|([.\w\d]+)))\s*(\{(.*)\}|\[(.*)\])?"\s+(Pos\s+((\d.)+|NaN))(NOEDIT)?/)
{
my $grpmatch = $2;
my $pos = $10;
if ($pos eq "NaN") {
$pos = 0;
print "Warning: Nan encountered for Contig position \n";
}
$_contigs{$ctgname}{'chr_remark'} = $6;
$_contigs{$ctgname}{'position'} = $pos;
$_contigs{$ctgname}{'subgroup'} = 0;
if (defined($grpmatch)) {
$_contigs{$ctgname}{'anchor'} = 1;
if ($grpmatch =~ /((\d+)((\D\d.\d+)|(.\d+)))|((\w+)(\.\d+))/) {
my ($group,$subgroup);
$group = $2 if($grpabbr eq "Chr");
$subgroup = $3 if($grpabbr eq "Chr");
$group = $7 if($grpabbr eq "Lg");
$subgroup = $8 if($grpabbr eq "Lg");
$subgroup = substr($subgroup,1) if ($subgroup =~ /^\./);
$_contigs{$ctgname}{'group'} = $group;
$_contigs{$ctgname}{'subgroup'} = $subgroup;
}
else {
$_contigs{$ctgname}{'group'} = $grpmatch;
}
}
else {
$_contigs{$ctgname}{'anchor'} = 1;
$_contigs{$ctgname}{'group'} = "?";
}
}
$curContig++;
print "Adding Contig $curContig...\n"
if ($self->verbose() && $curContig % 100 == 0);
}
$map->_setContigRef(\%_contigs);
$map->_calc_markerposition();
$map->_calc_contigposition() if ($map->version() < 7.0);
$map->_calc_contiggroup() if ($map->version() == 4.6);
return $map;
}
=head2 write_map
Title : write_map
Usage : $mapio->write_map($map);
Function: Write a map out
Returns : none
Args : Bio::Map::MapI
=cut
sub write_map{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
1;
=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
the Bioperl mailing list. 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<bioperl-l@bioperl.org>
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
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Gaurav Gupta
Email gaurav@genome.arizona.edu
=head1 PROJECT LEADERS
Jamie Hatfield jamie@genome.arizona.edu
Dr. Cari Soderlund cari@genome.arizona.edu
=head1 PROJECT DESCRIPTION
The project was done in Arizona Genomics Computational Laboratory
(AGCoL) at University of Arizona.
This work was funded by USDA-IFAFS grant #11180 titled "Web Resources
for the Computation and Display of Physical Mapping Data".
For more information on this project, please refer:
http://www.genome.arizona.edu
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut