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#!/usr/bin/env perl
use FindBin qw($RealBin);
use lib (($ENV{SOI_ROOT}) ||
(($INC[0]=~/^\./)?"$RealBin/$INC[0]":"$RealBin/.."));
use strict;
use SOI::Adapter;
use Getopt::Long;
use Carp;
use FileHandle;
my ($ad);
my $h = {};
GetOptions($h,
"dbname|d=s",
"program=s@",
"sourcename=s@",
"extend=s",
"format=s",
"debug",
);
my $dbname = $h->{dbname};
my $type = 'scaffold';
eval {
$ad = SOI::Adapter->new($dbname);
};
if ($@) {
print STDERR "There was an error\n";
print STDERR $@;
exit 1;
}
foreach my $seg (@ARGV) {
my ($features, $range, $t);
($range, $features) = &get_type_features($ad, $type, $seg);
if (@{$features || []}) {
my $arm = $ad->get_f({range=>$range}, {feature_types=>'chromosome_arm',noauxillaries=>1});
my ($fmin, $fmax) = ($range->{fmin},$range->{fmax});
my $new_f = $arm->stitch_child_segments($fmin,$fmax);
$arm->hash->{residues} = "";
my $rset_constr = {range=>$range};
$rset_constr->{program} = $h->{program} if ($h->{program});
$rset_constr->{sourcename} = $h->{sourcename} if ($h->{sourcename});
my $rsets = $ad->get_results($rset_constr);
map{$_->transform($new_f)}(@{$features},@{$rsets || []});
my $ans = $ad->get_analysis();
my %an_h;
map{$an_h{$_->analysis_id}=$_}@{$ans || []};
foreach my $rset (@{$rsets || []}) {
my $an = $an_h{$rset->analysis_id};
$an->add_node($rset) if ($an);
}
$arm->nodes([@{$arm->nodes || []},@{$features}, @{$ans || []}]);
my $format = $h->{format} || "soi";
my $m = "to_$format"."_xml";
my $f;
$f = "$seg.$format.xml" unless (scalar(@ARGV) == 1);
$arm->$m($f);
}
else {
printf STDERR "did not get any feature for %s=%s\n", $type, $seg
}
}
$ad->close_handle;
exit;
sub get_type_features {
my $ad = shift;
my $by_type = shift;
my $type = $by_type;
my $val = shift;
my $opts = {};
if ($by_type eq 'gene') {
$opts->{extend} = $h->{extend} || 50000;
}
my $method = "get_features_by_$type";
if ($ad->can($method)) {
return ($ad->$method($val, $opts));
}
else {
confess("can not do $method");
}
}
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