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Commit c0930f9c authored by Nathan Johnson's avatar Nathan Johnson
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just some tidyup

parent 80aa6f99
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Showing with 45 additions and 74 deletions
misc-scripts/probe_mapping/probe2transcript.pl
View file @ c0930f9c
......@@ -8,7 +8,7 @@
#Change all probe specific unmapped object to reeflect the individual probe rather than the probeset
#Updated logs
#Updated docs
#Added control of promiscuous probesets and unmapped object ????
#Added control of promiscuous probesets and unmapped objects
use strict;
......@@ -20,15 +20,29 @@ use Bio::EnsEMBL::UnmappedObject;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Mapper::RangeRegistry;
my ($transcript_host, $transcript_port, $transcript_user, $transcript_pass, $transcript_dbname,
$oligo_host, $oligo_port, $oligo_user, $oligo_pass, $oligo_dbname, $five_utr, $three_utr,
$xref_host, $xref_port, $xref_user, $xref_pass, $xref_dbname, $force_delete,
$max_mismatches, $utr_length, $max_transcripts_per_probeset, $max_transcripts, @arrays, $delete,
$mapping_threshold, $no_triage, $health_check);
#my $first_cache = 1;
#$| = 1; # auto flush stdout
GetOptions('transcript_host=s' => \$transcript_host,
my ($transcript_host, $transcript_user, $transcript_pass, $transcript_dbname,
$oligo_host, $oligo_user, $oligo_pass, $oligo_dbname, $five_utr, $three_utr,
$xref_host, $xref_user, $xref_pass, $xref_dbname, $force_delete,
$max_transcripts, @arrays, $delete, $no_triage, $health_check);
my ($oligo_db, $xref_db, %promiscuous_probesets, %transcripts_per_probeset, @unmapped_objects, $um_obj,
%transcript_ids , %transcript_probeset_count, %arrays_per_probeset, %array_probeset_sizes);
# Default options
my $transcript_port = 3306;
my $oligo_port = 3306;
my $xref_port = 3306;
my $max_mismatches = 1;
my $utr_length = 2000;
my $max_transcripts_per_probeset = 100;
my $mapping_threshold = 0.5;
GetOptions(
'transcript_host=s' => \$transcript_host,
'transcript_user=s' => \$transcript_user,
'transcript_port=i' => \$transcript_port,
'transcript_pass=s' => \$transcript_pass,
......@@ -53,16 +67,10 @@ GetOptions('transcript_host=s' => \$transcript_host,
'force_delete' => \$force_delete,
'no_triage' => \$no_triage,
'health_check' => \$health_check,
'help' => sub { usage(); exit(0); });
'help' => sub { usage(); exit(0); }
);
# Default options
$transcript_port ||= 3306; $oligo_port ||= 3306; $xref_port ||= 3306;
$max_mismatches ||= 1;
$utr_length ||= 2000;
@arrays = split(/,/,join(',',@arrays));#?
if(($utr_length =~ /\D/) && ($utr_length ne 'annotated')){
die("Invalid utr_length parameter($utr_length). Must be a number or 'annotated'");
......@@ -71,14 +79,9 @@ else{
$three_utr = $utr_length;
}
$max_transcripts_per_probeset ||= 100;
$mapping_threshold ||= 0.5;
@arrays = split(/,/,join(',',@arrays));#?
usage() if(!$transcript_user || !$transcript_dbname || !$transcript_host);
print 'Running on probe2trascript.pl on: '.`hostname`."\n";
my $transcript_db = new Bio::EnsEMBL::DBSQL::DBAdaptor('-host' => $transcript_host,
......@@ -86,7 +89,6 @@ my $transcript_db = new Bio::EnsEMBL::DBSQL::DBAdaptor('-host' => $transcript_
'-user' => $transcript_user,
'-pass' => $transcript_pass,
'-dbname' => $transcript_dbname);
my $oligo_db;
if ($oligo_host && $oligo_dbname && $oligo_user) {
......@@ -103,7 +105,6 @@ if ($oligo_host && $oligo_dbname && $oligo_user) {
}
my $xref_db;
if ($xref_host && $xref_dbname && $xref_user) {
......@@ -145,18 +146,6 @@ my $unmapped_object_adaptor = $xref_db->get_UnmappedObjectAdaptor();
my $analysis = get_or_create_analysis($analysis_adaptor);
my %promiscuous_probesets;
my %transcripts_per_probeset;
my %transcript_ids;
my %transcript_probeset_count; # key: transcript:probeset value: count
my %arrays_per_probeset;
my %array_probeset_sizes;
my @unmapped_objects;
$| = 1; # auto flush stdout
my $um_obj;#globally defined.
my $i = 0;
my $last_pc = -1;
......@@ -372,54 +361,36 @@ foreach my $key (keys %transcript_probeset_count) {
add_xref($transcript_ids{$transcript}, $probeset, $db_entry_adaptor, $array, $probeset_size, $hits);
print LOG "$probeset\t$transcript\tmapped\t$probeset_size\t$hits\n";
} else {
}
else {
print LOG "$probeset\t$transcript\tpromiscuous\t$probeset_size\t$hits\tCurrentTranscripts".$transcripts_per_probeset{$probeset}."\n";
push @{$promiscuous_probesets{$probeset}}, $transcript_ids{$transcript};
#$um_obj = new Bio::EnsEMBL::UnmappedObject(-type => 'probe2transcript',
# -analysis => $analysis,
# -identifier => $probeset,
# -summary => "Promiscuous probeset",
# -full_desc => "Probeset maps to greater than 100 transcripts",
# -ensembl_object_type => 'Transcript',
# -ensembl_id => $transcript_ids{$transcript});
#
#&cache_and_load_unmapped_objects($um_obj);
# TODO - remove mappings for probesets that end up being promiscuous
}
# TODO - write insufficient/promiscuous/orphan to unmapped_object ?
} else {
}
else {
print LOG "$probeset\t$transcript\tinsufficient\t$probeset_size\t$hits\n";
if (!$no_triage) {
#Can/should we concentrate all unmapped info into one record
#Currently getting one for each probe and each probeset
$um_obj = new Bio::EnsEMBL::UnmappedObject(-type => 'probe2transcript',
-analysis => $analysis,
-identifier => $probeset,
-summary => "Insufficient hits",
-full_desc => "Probeset had an insufficient number of hits (probeset size = $probeset_size, hits = $hits)",
-ensembl_object_type => 'Transcript',
-ensembl_id => $transcript_ids{$transcript});
if (!$no_triage) {
&cache_and_load_unmapped_objects($um_obj);
#Can/should we concentrate all unmapped info into one record
#Currently getting one for each probe and each probeset
$um_obj = new Bio::EnsEMBL::UnmappedObject(-type => 'probe2transcript',
-analysis => $analysis,
-identifier => $probeset,
-summary => "Insufficient hits",
-full_desc => "Probeset had an insufficient number of hits (probeset size = $probeset_size, hits = $hits)",
-ensembl_object_type => 'Transcript',
-ensembl_id => $transcript_ids{$transcript});
&cache_and_load_unmapped_objects($um_obj);
}
}
}
}
......
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