Bio::MapIO fpc
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Summary
Bio::MapIO::fpc - A FPC Map reader
Package variables
Privates (from "my" definitions)
$_readcor;
Included modules
Bio::Map::Clone
Bio::Map::Contig
Bio::Map::FPCMarker
Bio::Map::Physical
Bio::Range
POSIX
Inherit
Bio::MapIO
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. }
Description
This object contains code for parsing and processing FPC files and creating
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.
Methods
_initializeDescriptionCode
next_mapDescriptionCode
write_mapDescriptionCode
Methods description
_initializecode    nextTop
 Title   : _initialize
Usage : called implicitly
Function: calls the SUPER::_initialize
Returns : nothing
Args : species, readcor
next_mapcodeprevnextTop
 Title   : next_map
Usage : my $fpcmap = $mapio->next_map();
Function: gets the fpcmap from MapIO
Returns : object of type Bio::Map::MapI
Args : none
write_mapcodeprevnextTop
 Title   : write_map
Usage : $mapio->write_map($map);
Function: Write a map out
Returns : none
Args : Bio::Map::MapI
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my ($self,@args) = @_;
    my $species;
    $self->SUPER::_initialize(@args);
    ($species,$_readcor) = $self->_rearrange([qw(SPECIES READCOR)], @args);
    $_readcor = 0 unless (defined($_readcor));
}
next_mapdescriptionprevnextTop
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($filename)-3)."cor";
        if (open(CORE,$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 $map;
}
write_mapdescriptionprevnextTop
sub write_map {
    my ($self,@args) = @_;
    $self->throw_not_implemented();
}

1;
}
General documentation
InitializerTop
Access MethodsTop
These methods let you get and set the member variables
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Gaurav GuptaTop
Email gaurav@genome.arizona.edu
PROJECT LEADERSTop
Jamie Hatfield jamie@genome.arizona.edu
Dr. Cari Soderlund cari@genome.arizona.edu
PROJECT DESCRIPTIONTop
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
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _