Raw content of Bio::EnsEMBL::Analysis::Config::ProbeAlign
<![CDATA[#
# package Bio::EnsEMBL::Analysis::Config::Funcgen::ProbeAlign?
#
# Cared for by EnsEMBL (ensembl-dev@ebi.ac.uk)
#
# Copyright GRL & EBI
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::Analysis::Config::Funcgen::ProbeAlign?
=head1 SYNOPSIS
use Bio::EnsEMBL::Analysis::Config::Funcgen::ProbeAlign;
=head1 DESCRIPTION
This contains the configuration for step 2 of the
process which maps probes to a Genome. This step
is an alignment of probes (dna) against a genome (dna)
using exonerate. So this config looks very similar to that
of any other exonerate-driving config.
The layout of the configuration is a set of hashes,
each one keyed by logic name. There is also a DEFAULT hash,
which is used as the default for all logic names.
There are genomic and transcript based logic names and config
hashes for each discrete format of array.
=head1 CONTACT
=cut
package Bio::EnsEMBL::Analysis::Config::ProbeAlign;
use strict;
use vars qw( %Config );
%Config =
(
#This entire hash is exported as the global $PROBE_CONFIG var
#each key will be exported as $PROBE_CONFIG->{'_CONFIG_'.$key}
#Dependant on logic name of RunnableDB
PROBE_CONFIG =>
{
DEFAULT =>
{
# path to softmasked, dusted genomic sequence or transcript seqs on the farm
# #'/data/blastdb/Ensembl/Rmacaque/MMUL_2/genome/softmasked_dusted.fa',
#/data/blastdb/Ensembl/Human/NCBI35/softmasked_dusted/', #allowed to be a dir.
TARGETSEQS => $ENV{'GENOMICSEQS'},#or $ENV{'TRANSCRIPTSEQS'}
QUERYTYPE => 'dna',
# must be a single file containing all (non-redundant) probes indexed by affy_probe_id
# QUERYSEQS refers to the value of the parameter NON_REDUNDANT_PROBE_SEQS
# in the config-file ensembl-analysis/Config/CollapseAffyProbes.pm
#QUERYSEQS => $ENV{'NR_FASTA'},
#Removed this now as we want to run different analyses at the same time so we have to hardcode below
# must supply one, since the queryseqs MUST be a single file
#InputIDREGEXP this is used to infer chunk number from the headers of a single fasta file
#Therefore we cannot have mixed type in the same file, must be in a different array set
#If not related, or reformated prior to Import if they are related
IIDREGEXP => '(\d+):(\d+)',
#DNADB is not essential, but we need this if we are going to define a DNADB not on ensembldb
#e.g. new release on staging
#Add species and group here?
DNADB => {
-dbname => $ENV{'DNADB_NAME'},
-host => $ENV{'DNADB_HOST'},
-port => $ENV{'DNADB_PORT'},
-user => $ENV{'DNADB_USER'},
-pass => $ENV{'DNADB_PASS'},
-species => $ENV{'SPECIES'},
-multispecies_db => $ENV{'DNADB_MULTISPECIES_DB'},
-species_id => $ENV{'DNADB_SPECIES_ID'}
},
OUTDB => {
-dbname => $ENV{'DB_NAME'},
-host => $ENV{'DB_HOST'},
-port => $ENV{'DB_PORT'},
-user => $ENV{'DB_USER'},
-pass => $ENV{'DB_PASS'},
-species => $ENV{'SPECIES'},#required for auto generation fo DNADB
-multispecies_db => $ENV{'MULTISPECIES_DB'},
-species_id => $ENV{'SPECIES_ID'}
},
#25 mers
OPTIONS => ' --bestn 100 --dnahspthreshold 116 --fsmmemory 256 --dnawordlen 25 --dnawordlimit 11 ',
#50 mers
#OPTIONS => ' --bestn 100 --dnahspthreshold 116 --fsmmemory 256 --dnawordlen 50 --dnawordthreshold 11 ',
# if the number of hits reaches or exceeds the figure below, we reject
# all hits to that probe
HIT_SATURATION_LEVEL => 100,#2 for unique tiling arrays mappings
MAX_MISMATCHES => 1,#No way to dynamically test method prerequisite config vars without setting a FILTER_METHOD hash?
#This would not be bullet proof a the hash could then be edited
#Would need to add another method to Runnable::ExonerateProbe to change this
#FILTER_METHOD => 'filter_mismatches',
#Or we can pass a code ref here to allow easy extension without editing Runnables etc.
#Can't name code ref subs!
#This is used in ExonerateProbe.pm
#e.g.
#FILTER_METHOD => sub {
# my ($self, $query_match_length, $q_length, $score) = @_;
# my $mismatch;
# my $full_score = $q_length * 5;
# if($query_match_length == $q_length){
# if($score == $full_score){
# $mismatch = 0;
# }
# }
# if(! defined $mismatch){
# my $max_mismatch = $self->allowed_mismatches;
# for my $i(1..$max_mismatch){
# my $mismatch_length = $q_length - $i;
# my $mismatch_score = $mismatch_length * 5;
# if($query_match_length == $q_length){
# if ($score == ($full_score - ($i*9))) {
# $mismatch = $i;
# }
# }
# elsif($query_match_length == $mismatch_length){
# $mismatch = $i if ($score == $mismatch_score);
# }
# }
# }
# return $mismatch;
#},
},#end of DEFAULT
#IIDREGEXP, DNADB, OUTDB and QUERYSEQS and QUERYTYPE should be same for all these configs
#Need to add ILLUMINA_PROBE_ALIGN, ILLUMINA_PROBE_TRANSCRIPT_ALIGN, CODELINK, AGILENT etc
#There is no point in using a % threshold here as bestn value will most likely cause only high quality
#hits to be returned. However there is a possiblity with longer sequences that we may get a duff alignment.
#We could set -percent to a conservative 95%, but this entirely depends on the length and number of allowed
#mismatches.
#Define QUERYSEQS here instead of in Runnable to prevent convolution
#of RunnableDB and environment,
#i.e. we can still run ProbeAlign so long as we change this config
#The only downfall is lack of validation of QUERYSEQS files
#WARNING CHECK YOUR QUERYSEQS!
AFFY_UTR_PROBEALIGN =>
{
MAX_MISMATCHES => 1,
TARGETSEQS => $ENV{'GENOMICSEQS'},
QUERYSEQS => $ENV{'WORK_DIR'}.'/arrays_nr.AFFY_UTR.fasta',
#at least 25 mers allowing 1bp mismatch
#this will still work in the worst case where the mismatch is at the centre of a 25bp probe
OPTIONS => ' --bestn 101 --fsmmemory 256 --dnawordlen 12 --seedrepeat 2 --dnahspthreshold 118 --dnawordlimit 0',
#OPTIONS => ' --bestn 101 --dnahspthreshold 116 --fsmmemory 256 --dnawordlen 14 --dnawordlimit 11 ',
HIT_SATURATION_LEVEL => 100,
},
#Essentially same as AFFY but with different NR_FASTA
AFFY_ST_PROBEALIGN =>
{
TARGETSEQS => $ENV{'GENOMICSEQS'},
QUERYSEQS => $ENV{'WORK_DIR'}.'/arrays_nr.AFFY_ST.fasta',
#25 mers
#OPTIONS => ' --bestn 101 --dnahspthreshold 116 --fsmmemory 256 --dnawordlen 14 --dnawordlimit 11 ',
OPTIONS => ' --bestn 101 --fsmmemory 256 --dnawordlen 12 --seedrepeat 2 --dnahspthreshold 118 --dnawordlimit 0',
HIT_SATURATION_LEVEL => 100,
MAX_MISMATCHES => 1,
},
NIMBLEGEN_PROBEALIGN =>
{
TARGETSEQS => $ENV{'GENOMICSEQS'},
#Need to define this dynamically based on oligo length (40-60mers)
#50mers
#Can we up the dnaword limit 10 50 here if we only want unique matches?
OPTIONS => ' --bestn 2 --dnahspthreshold 116 --fsmmemory 256 --dnawordlen 50 --dnawordlimit 11 ',
HIT_SATURATION_LEVEL => 2, #We only want unique mappings for tiling probes
MAX_MISMATCHES => 0, #Unique mappings for tiling probes
},
#ILLUMINA_WG are 51mers. These settings allow for at least 1bp mismatch
ILLUMINA_WG_PROBEALIGN =>
{
TARGETSEQS => $ENV{'GENOMICSEQS'},
QUERYSEQS => $ENV{'WORK_DIR'}.'/arrays_nr.ILLUMINA_WG.fasta',
#Need to define this dynamically based on oligo length (40-60mers)
#50mers
OPTIONS => ' --bestn 101 --dnahspthreshold 246 --fsmmemory 256 --dnawordlen 25 --seedrepeat 2 --dnawordlimit 0 ',
HIT_SATURATION_LEVEL => 100,
MAX_MISMATCHES => 1, #Unique mappings for tiling probes
},
ILLUMINA_WG_PROBETRANSCRIPTALIGN =>
{
TARGETSEQS => $ENV{'TRANSCRIPTSEQS'},
QUERYSEQS => $ENV{'WORK_DIR'}.'/arrays_nr.ILLUMINA_WG.fasta',
#Need to define this dynamically based on oligo length (40-60mers)
#50mers
OPTIONS => ' --bestn 101 --dnahspthreshold 246 --fsmmemory 256 --dnawordlen 25 --seedrepeat 2 --dnawordlimit 0 ',
HIT_SATURATION_LEVEL => 100,
MAX_MISMATCHES => 1, #Unique mappings for tiling probes
},
#CODELINK are 30mers
CODELINK_WG_PROBEALIGN =>
{
TARGETSEQS => $ENV{'GENOMICSEQS'},
QUERYSEQS => $ENV{'WORK_DIR'}.'/arrays_nr.CODELINK.fasta',
OPTIONS => ' --bestn 101 --dnahspthreshold 246 --fsmmemory 256 --dnawordlen 15 --seedrepeat 2 --dnawordlimit 0 ',
HIT_SATURATION_LEVEL => 100,
MAX_MISMATCHES => 1, #Unique mappings for tiling probes
},
CODELINK_WG_PROBETRANSCRIPTALIGN =>
{
TARGETSEQS => $ENV{'TRANSCRIPTSEQS'},
QUERYSEQS => $ENV{'WORK_DIR'}.'/arrays_nr.CODELINK.fasta',
OPTIONS => ' --bestn 101 --dnahspthreshold 246 --fsmmemory 256 --dnawordlen 15 --seedrepeat 2 --dnawordlimit 0 ',
HIT_SATURATION_LEVEL => 100,
MAX_MISMATCHES => 1, #Unique mappings for tiling probes
},
#PHALANX are 60mers
PHALANX_WG_PROBEALIGN =>
{
TARGETSEQS => $ENV{'GENOMICSEQS'},
QUERYSEQS => $ENV{'WORK_DIR'}.'/arrays_nr.PHALANX.fasta',
OPTIONS => ' --bestn 101 --dnahspthreshold 246 --fsmmemory 256 --dnawordlen 30 --seedrepeat 2 --dnawordlimit 0 ',
HIT_SATURATION_LEVEL => 100,
MAX_MISMATCHES => 1, #Unique mappings for tiling probes
},
PHALANX_WG_PROBETRANSCRIPTALIGN =>
{
TARGETSEQS => $ENV{'TRANSCRIPTSEQS'},
QUERYSEQS => $ENV{'WORK_DIR'}.'/arrays_nr.PHALANX.fasta',
OPTIONS => ' --bestn 101 --dnahspthreshold 246 --fsmmemory 256 --dnawordlen 30 --seedrepeat 2 --dnawordlimit 0 ',
HIT_SATURATION_LEVEL => 100,
MAX_MISMATCHES => 1, #Unique mappings for tiling probes
},
AFFY_UTR_PROBETRANSCRIPTALIGN =>
{
TARGETSEQS => $ENV{'TRANSCRIPTSEQS'},
QUERYSEQS => $ENV{'WORK_DIR'}.'/arrays_nr.AFFY_UTR.fasta',
#25 mers
OPTIONS => ' --bestn 101 --fsmmemory 256 --dnawordlen 12 --seedrepeat 2 --dnahspthreshold 118 --dnawordlimit 0',
#OPTIONS => ' --bestn 101 --dnahspthreshold 116 --fsmmemory 256 --dnawordlen 14 --dnawordlimit 11 ',
#HIT_SATURATION_LEVEL => 100,#I don't think we want this for the transcript mappings
#Defaults to 100 anyway, but not used
#FILTER_METHOD => 'filter_mismatches',#Would need to add another method to Runnable::Exonerate
MAX_MISMATCHES => 1,
},
#Essentially same as AFFY but with different NR_FASTA
AFFY_ST_PROBETRANSCRIPTALIGN =>
{
TARGETSEQS => $ENV{'TRANSCRIPTSEQS'},
QUERYSEQS => $ENV{'WORK_DIR'}.'/arrays_nr.AFFY_ST.fasta',
#25 mers
OPTIONS => ' --bestn 101 --fsmmemory 256 --dnawordlen 12 --seedrepeat 2 --dnahspthreshold 118 --dnawordlimit 0',
#OPTIONS => ' --bestn 101 --dnahspthreshold 116 --fsmmemory 256 --dnawordlen 14 --dnawordlimit 11 ',
#HIT_SATURATION_LEVEL => 100,
MAX_MISMATCHES => 1,
},
#AGILENT 60 mers
AGILENT_PROBEALIGN =>
{
TARGETSEQS => $ENV{'GENOMICSEQS'},
QUERYSEQS => $ENV{'WORK_DIR'}.'/arrays_nr.AGILENT.fasta',
OPTIONS => ' --bestn 101 --dnahspthreshold 246 --fsmmemory 256 --dnawordlen 30 --seedrepeat 2 --dnawordlimit 0 ',
HIT_SATURATION_LEVEL => 100,
MAX_MISMATCHES => 1,
},
AGILENT_PROBETRANSCRIPTALIGN =>
{
TARGETSEQS => $ENV{'TRANSCRIPTSEQS'},
QUERYSEQS => $ENV{'WORK_DIR'}.'/arrays_nr.AGILENT.fasta',
OPTIONS => ' --bestn 101 --dnahspthreshold 246 --fsmmemory 256 --dnawordlen 30 --seedrepeat 2 --dnawordlimit 0 ',
HIT_SATURATION_LEVEL => 100,
MAX_MISMATCHES => 1,
},
#LEIDEN 50 mers
LEIDEN_PROBEALIGN =>
{
TARGETSEQS => $ENV{'GENOMICSEQS'},
QUERYSEQS => $ENV{'WORK_DIR'}.'/arrays_nr.LEIDEN.fasta',
OPTIONS => ' --bestn 101 --dnahspthreshold 246 --fsmmemory 256 --dnawordlen 25 --seedrepeat 2 --dnawordlimit 0 ',
HIT_SATURATION_LEVEL => 100,
MAX_MISMATCHES => 1,
},
LEIDEN_PROBETRANSCRIPTALIGN =>
{
TARGETSEQS => $ENV{'TRANSCRIPTSEQS'},
QUERYSEQS => $ENV{'WORK_DIR'}.'/arrays_nr.LEIDEN.fasta',
OPTIONS => ' --bestn 101 --dnahspthreshold 246 --fsmmemory 256 --dnawordlen 25 --seedrepeat 2 --dnawordlimit 0 ',
HIT_SATURATION_LEVEL => 100,
MAX_MISMATCHES => 1,
},
}
);
sub import {
my ($callpack) = caller(0); # Name of the calling package
my $pack = shift; # Need to move package off @_
# Get list of variables supplied, or else everything
my @vars = @_ ? @_ : keys( %Config );
return unless @vars;
# Predeclare global variables in calling package
eval "package $callpack; use vars qw("
. join(' ', map { '$'.$_ } @vars) . ")";
die $@ if $@;
foreach (@vars) {
if ( defined $Config{$_} ) {
no strict 'refs';
# Exporter does a similar job to the following
# statement, but for function names, not
# scalar variables:
*{"${callpack}::$_"} = \$Config{ $_ };
} else {
die "Error: Config: $_ not known\n";
}
}
}
1;
]]>