From 23c5faec874ee16ab172977552c7f41939347a60 Mon Sep 17 00:00:00 2001
From: Patrick Meidl <pm2@sanger.ac.uk>
Date: Fri, 4 Apr 2008 14:49:05 +0000
Subject: [PATCH] changed param dumppath to basedir
---
misc-scripts/id_mapping/default.conf | 4 +--
misc-scripts/id_mapping/dump_by_seq_region.pl | 4 +--
misc-scripts/id_mapping/dump_cache.pl | 4 +--
misc-scripts/id_mapping/id_mapping.pl | 4 +--
misc-scripts/id_mapping/synteny_rescore.pl | 8 +++---
.../id_mapping/utils/compare_results.pl | 6 ++--
.../id_mapping/utils/compare_scores.pl | 4 +--
misc-scripts/id_mapping/utils/dump_scores.pl | 10 +++----
modules/Bio/EnsEMBL/IdMapping/BaseObject.pm | 18 ++++++------
modules/Bio/EnsEMBL/IdMapping/Cache.pm | 2 +-
.../Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm | 28 +++++++++----------
.../Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm | 4 +--
.../Bio/EnsEMBL/IdMapping/InternalIdMapper.pm | 22 +++++++--------
.../Bio/EnsEMBL/IdMapping/ResultAnalyser.pm | 2 +-
modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm | 2 +-
.../Bio/EnsEMBL/IdMapping/StableIdMapper.pm | 4 +--
.../Bio/EnsEMBL/IdMapping/SyntenyFramework.pm | 4 +--
.../IdMapping/TranscriptScoreBuilder.pm | 4 +--
18 files changed, 67 insertions(+), 67 deletions(-)
diff --git a/misc-scripts/id_mapping/default.conf b/misc-scripts/id_mapping/default.conf
index d8237a4708..f54b6f6e71 100644
--- a/misc-scripts/id_mapping/default.conf
+++ b/misc-scripts/id_mapping/default.conf
@@ -5,10 +5,10 @@ dry_run = 0
loglevel = DEBUG
; paths
-dumppath = /lustre/scratch1/ensembl/pm2/idmapping/perl/2008-04-01
+basedir = /lustre/work1/ensembl/pm2/idmapping/perl/2008-04-01
; prepend this path to your 'log' parameter
-; will default to "$dumppath/log" if not set
+; will default to "$basedir/log" if not set
;logpath = /lustre/scratch1/ensembl/pm2/idmapping/log_20070823
; old db settings
diff --git a/misc-scripts/id_mapping/dump_by_seq_region.pl b/misc-scripts/id_mapping/dump_by_seq_region.pl
index 9e955aa3d0..3bde6d4a72 100755
--- a/misc-scripts/id_mapping/dump_by_seq_region.pl
+++ b/misc-scripts/id_mapping/dump_by_seq_region.pl
@@ -74,7 +74,7 @@ $conf->parse_options(
'targetuser|target_user=s' => 1,
'targetpass|target_pass=s' => 0,
'targetdbname|target_dbname=s' => 1,
- 'dumppath|dump_path=s' => 1,
+ 'basedir|basedir=s' => 1,
'biotypes=s@' => 0,
'dbtype=s' => 1,
'slice_name=s' => 1,
@@ -83,7 +83,7 @@ $conf->parse_options(
# set default logpath
unless ($conf->param('logpath')) {
- $conf->param('logpath', path_append($conf->param('dumppath'), 'log'));
+ $conf->param('logpath', path_append($conf->param('basedir'), 'log'));
}
# log to a subdirectory to prevent clutter
$conf->param('logpath', path_append($conf->param('logpath'),
diff --git a/misc-scripts/id_mapping/dump_cache.pl b/misc-scripts/id_mapping/dump_cache.pl
index eb144ded2a..e6c9687223 100755
--- a/misc-scripts/id_mapping/dump_cache.pl
+++ b/misc-scripts/id_mapping/dump_cache.pl
@@ -84,7 +84,7 @@ $conf->parse_options(
'targetuser|target_user=s' => 1,
'targetpass|target_pass=s' => 0,
'targetdbname|target_dbname=s' => 1,
- 'dumppath|dump_path=s' => 1,
+ 'basedir|basedir=s' => 1,
'chromosomes|chr=s@' => 0,
'region=s' => 0,
'biotypes=s@' => 0,
@@ -93,7 +93,7 @@ $conf->parse_options(
# set default logpath
unless ($conf->param('logpath')) {
- $conf->param('logpath', path_append($conf->param('dumppath'), 'log'));
+ $conf->param('logpath', path_append($conf->param('basedir'), 'log'));
}
# get log filehandle and print heading and parameters to logfile
diff --git a/misc-scripts/id_mapping/id_mapping.pl b/misc-scripts/id_mapping/id_mapping.pl
index 5a9fedb734..b21fd69057 100755
--- a/misc-scripts/id_mapping/id_mapping.pl
+++ b/misc-scripts/id_mapping/id_mapping.pl
@@ -77,7 +77,7 @@ my $conf = new Bio::EnsEMBL::Utils::ConfParser(
$conf->parse_options(
'mode=s' => 0,
- 'dumppath|dump_path=s' => 1,
+ 'basedir|basedir=s' => 1,
'chromosomes|chr=s@' => 0,
'region=s' => 0,
'biotypes=s@' => 0,
@@ -94,7 +94,7 @@ $conf->parse_options(
# set default logpath
unless ($conf->param('logpath')) {
- $conf->param('logpath', path_append($conf->param('dumppath'), 'log'));
+ $conf->param('logpath', path_append($conf->param('basedir'), 'log'));
}
# get log filehandle and print heading and parameters to logfile
diff --git a/misc-scripts/id_mapping/synteny_rescore.pl b/misc-scripts/id_mapping/synteny_rescore.pl
index 42260894ef..c39fa92ccc 100755
--- a/misc-scripts/id_mapping/synteny_rescore.pl
+++ b/misc-scripts/id_mapping/synteny_rescore.pl
@@ -67,7 +67,7 @@ my $conf = new Bio::EnsEMBL::Utils::ConfParser(
);
$conf->parse_options(
- 'dumppath|dump_path=s' => 1,
+ 'basedir|basedir=s' => 1,
'index|i=n' => 1,
);
@@ -95,10 +95,10 @@ my $cache = Bio::EnsEMBL::IdMapping::Cache->new(
$cache->read_instance_from_file;
# load SyntenyFramework and gene ScoredMappingMatrix from files
-my $dump_path = $conf->param('dumppath');
+my $basedir = $conf->param('basedir');
my $sf = Bio::EnsEMBL::IdMapping::SyntenyFramework->new(
- -DUMP_PATH => path_append($dump_path, 'mapping'),
+ -DUMP_PATH => path_append($basedir, 'mapping'),
-CACHE_FILE => 'synteny_framework.ser',
-LOGGER => $logger,
-CONF => $conf,
@@ -107,7 +107,7 @@ my $sf = Bio::EnsEMBL::IdMapping::SyntenyFramework->new(
$sf->read_from_file;
my $gene_scores = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
- -DUMP_PATH => path_append($dump_path, 'matrix/synteny_rescore'),
+ -DUMP_PATH => path_append($basedir, 'matrix/synteny_rescore'),
-CACHE_FILE => "gene_matrix_synteny$index.ser",
-AUTO_LOAD => 1,
);
diff --git a/misc-scripts/id_mapping/utils/compare_results.pl b/misc-scripts/id_mapping/utils/compare_results.pl
index 83470e6df3..10f6eb5dd5 100755
--- a/misc-scripts/id_mapping/utils/compare_results.pl
+++ b/misc-scripts/id_mapping/utils/compare_results.pl
@@ -81,7 +81,7 @@ $conf->parse_options(
'altuser|alt_user=s' => 0,
'altpass|alt_pass=s' => 0,
'altdbname|alt_dbname=s' => 1,
- 'dumppath|dump_path=s' => 1,
+ 'basedir|basedir=s' => 1,
'lsf!' => 0,
'lsf_opt|lsfopt=s' => 0,
'suffix|sfx=s' => 0,
@@ -92,7 +92,7 @@ $conf->parse_options(
# set default logpath
unless ($conf->param('logpath')) {
- $conf->param('logpath', path_append($conf->param('dumppath'), 'log'));
+ $conf->param('logpath', path_append($conf->param('basedir'), 'log'));
}
# assume both dbs are on same host unless specified otherwise
@@ -196,7 +196,7 @@ sub compare_features {
my $ftype = shift;
# get a filehandle to write results for debugging
- my $path = path_append($conf->param('dumppath'), 'debug');
+ my $path = path_append($conf->param('basedir'), 'debug');
my $file = "$path/${ftype}_diff.txt";
open(my $fh, '>', $file) or die "Can't open $file for writing: $!\n";
diff --git a/misc-scripts/id_mapping/utils/compare_scores.pl b/misc-scripts/id_mapping/utils/compare_scores.pl
index e0e66b07b8..e1b5bd1a26 100755
--- a/misc-scripts/id_mapping/utils/compare_scores.pl
+++ b/misc-scripts/id_mapping/utils/compare_scores.pl
@@ -9,7 +9,7 @@
Required arguments:
- --dumppath=PATH base directory of ID mapping results
+ --basedir=PATH base directory of ID mapping results
Optional arguments:
@@ -67,7 +67,7 @@ $conf->parse_options(
# set default logpath
unless ($conf->param('logpath')) {
- $conf->param('logpath', path_append($conf->param('dumppath'), 'log'));
+ $conf->param('logpath', path_append($conf->param('basedir'), 'log'));
}
# get log filehandle and print heading and parameters to logfile
diff --git a/misc-scripts/id_mapping/utils/dump_scores.pl b/misc-scripts/id_mapping/utils/dump_scores.pl
index c3e1eed3fa..641483677e 100755
--- a/misc-scripts/id_mapping/utils/dump_scores.pl
+++ b/misc-scripts/id_mapping/utils/dump_scores.pl
@@ -10,7 +10,7 @@ dump_scores.pl [arguments]
Required arguments:
- --dumppath=PATH base directory of ID mapping results
+ --basedir=PATH base directory of ID mapping results
Optional arguments:
@@ -67,12 +67,12 @@ my $conf = new Bio::EnsEMBL::Utils::ConfParser(
);
$conf->parse_options(
- 'dumppath|dump_path=s' => 1,
+ 'basedir|basedir=s' => 1,
);
# set default logpath
unless ($conf->param('logpath')) {
- $conf->param('logpath', path_append($conf->param('dumppath'), 'log'));
+ $conf->param('logpath', path_append($conf->param('basedir'), 'log'));
}
# get log filehandle and print heading and parameters to logfile
@@ -89,7 +89,7 @@ my $logger = new Bio::EnsEMBL::Utils::Logger(
# initialise log
$logger->init_log($conf->list_param_values);
-my $dump_path = path_append($conf->param('dumppath'), 'matrix');
+my $dump_path = path_append($conf->param('basedir'), 'matrix');
# genes
my $gene_matrix = &read_matrix('gene');
@@ -145,7 +145,7 @@ sub dump_scores {
$logger->info("Dumping $type scores to file...\n", 0, 'stamped');
- my $debug_path = path_append($conf->param('dumppath'), 'debug');
+ my $debug_path = path_append($conf->param('basedir'), 'debug');
my $logfile = "$debug_path/${type}_scores.txt";
open(my $fh, '>', $logfile) or
diff --git a/modules/Bio/EnsEMBL/IdMapping/BaseObject.pm b/modules/Bio/EnsEMBL/IdMapping/BaseObject.pm
index cc949d5478..57acb7b3e4 100644
--- a/modules/Bio/EnsEMBL/IdMapping/BaseObject.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/BaseObject.pm
@@ -112,13 +112,13 @@ sub new {
=head2 get_filehandle
Arg[1] : String $filename - filename for filehandle
- Arg[2] : String $path_append - append subdirectory name to dumppath
+ Arg[2] : String $path_append - append subdirectory name to basedir
Arg[3] : String $mode - filehandle mode (<|>|>>)
Example : my $fh = $object->get_filehandle('mapping_stats.txt', 'stats',
'>');
print $fh "Stats:\n";
Description : Returns a filehandle to a file for reading or writing. The file
- is qualified with the dumppath defined in the configuration and
+ is qualified with the basedir defined in the configuration and
an optional subdirectory name.
Return type : filehandle
Exceptions : thrown on missing filename
@@ -136,7 +136,7 @@ sub get_filehandle {
throw("Need a filename for this filehandle.") unless (defined($filename));
- my $path = $self->conf->param('dumppath');
+ my $path = $self->conf->param('basedir');
$path = path_append($path, $path_append) if (defined($path_append));
$mode ||= '>';
@@ -151,7 +151,7 @@ sub get_filehandle {
=head2 file_exists
Arg[1] : String $filename - filename to test
- Arg[2] : Boolean $path_append - turn on pre-pending of dumppath
+ Arg[2] : Boolean $path_append - turn on pre-pending of basedir
Example : unless ($object->file_exists('gene_mappings.ser', 1)) {
$object->do_gene_mapping;
}
@@ -169,7 +169,7 @@ sub file_exists {
my $filename = shift;
my $path_append = shift;
- my $path = $self->conf->param('dumppath');
+ my $path = $self->conf->param('basedir');
$path = path_append($path, $path_append) if (defined($path_append));
return (-s "$path/$filename");
@@ -219,7 +219,7 @@ sub fetch_value_from_db {
'stable_id_event', 'stable_id_event_existing.txt');
Description : Dumps the contents of a db table to a tab-delimited file. The
dump file will be written to a subdirectory called 'tables'
- under the dumppath from your configuration.
+ under the basedir from your configuration.
Return type : Int - the number of rows dumped
Exceptions : thrown on wrong or missing arguments
Caller : general
@@ -285,7 +285,7 @@ sub dump_table_to_file {
'stable_id_event', 'stable_id_event_new.txt');
Description : Uploads a tab-delimited data file into a db table. The data file
will be taken from a subdirectory 'tables' under your configured
- dumppath. If the db table isn't empty and $no_check_empty isn't
+ basedir. If the db table isn't empty and $no_check_empty isn't
set, no data is uploaded (and a warning is issued).
Return type : Int - the number of rows uploaded
Exceptions : thrown on wrong or missing arguments
@@ -315,7 +315,7 @@ sub upload_file_into_table {
return;
}
- my $file = join('/', $self->conf->param('dumppath'), 'tables', $filename);
+ my $file = join('/', $self->conf->param('basedir'), 'tables', $filename);
my $r = 0;
if (-s $file) {
@@ -379,7 +379,7 @@ sub logger {
Arg[1] : (optional) Bio::EnsEMBL::Utils::ConfParser - the configuration
to set
- Example : my $dumppath = $object->conf->param('dumppath');
+ Example : my $basedir = $object->conf->param('basedir');
Description : Getter/setter for configuration object
Return type : Bio::EnsEMBL::Utils::ConfParser
Exceptions : none
diff --git a/modules/Bio/EnsEMBL/IdMapping/Cache.pm b/modules/Bio/EnsEMBL/IdMapping/Cache.pm
index 88fed170ec..f01e5385f0 100644
--- a/modules/Bio/EnsEMBL/IdMapping/Cache.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/Cache.pm
@@ -637,7 +637,7 @@ sub instance_file {
sub dump_path {
my $self = shift;
- $self->{'dump_path'} ||= path_append($self->conf->param('dumppath'), 'cache');
+ $self->{'dump_path'} ||= path_append($self->conf->param('basedir'), 'cache');
return $self->{'dump_path'};
}
diff --git a/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm b/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
index 990b6ce206..eb01e9ec7e 100644
--- a/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
@@ -71,7 +71,7 @@ sub score_exons {
# debug logging
if ($self->logger->loglevel eq 'debug') {
- $matrix->log('exon', $self->conf->param('dumppath'));
+ $matrix->log('exon', $self->conf->param('basedir'));
}
# log stats of combined matrix
@@ -90,7 +90,7 @@ sub score_exons {
sub overlap_score {
my $self = shift;
- my $dump_path = path_append($self->conf->param('dumppath'), 'matrix');
+ my $dump_path = path_append($self->conf->param('basedir'), 'matrix');
my $matrix = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
-DUMP_PATH => $dump_path,
@@ -139,7 +139,7 @@ sub exonerate_score {
throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
}
- my $dump_path = path_append($self->conf->param('dumppath'), 'matrix');
+ my $dump_path = path_append($self->conf->param('basedir'), 'matrix');
my $exonerate_matrix = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
-DUMP_PATH => $dump_path,
@@ -387,16 +387,16 @@ sub run_exonerate {
$self->logger->error("Can't create lsf log dir $logpath: $!\n");
# delete exonerate output from previous runs
- my $dumppath = $self->cache->dump_path;
+ my $dump_path = $self->cache->dump_path;
- opendir(DUMPDIR, $dumppath) or
- $self->logger->error("Can't open $dumppath for reading: $!");
+ opendir(DUMPDIR, $dump_path) or
+ $self->logger->error("Can't open $dump_path for reading: $!");
while (defined(my $file = readdir(DUMPDIR))) {
next unless /exonerate_map\.\d+/;
- unlink("$dumppath/$file") or
- $self->logger->error("Can't delete $dumppath/$file: $!");
+ unlink("$dump_path/$file") or
+ $self->logger->error("Can't delete $dump_path/$file: $!");
}
closedir(DUMPDIR);
@@ -422,7 +422,7 @@ sub run_exonerate {
qq{--percent $percent } .
$self->conf->param('exonerate_extra_params') . " " .
q{--ryo 'myinfo: %qi %ti %et %ql %tl\n' } .
- qq{| grep '^myinfo:' > $dumppath/exonerate_map.\$LSB_JOBINDEX} . "\n";
+ qq{| grep '^myinfo:' > $dump_path/exonerate_map.\$LSB_JOBINDEX} . "\n";
$self->logger->info("Submitting $num_jobs exonerate jobs to lsf.\n");
$self->logger->debug("$exonerate_job\n\n");
@@ -456,7 +456,7 @@ sub run_exonerate {
for (my $i = 1; $i <= $num_jobs; $i++) {
# check that output file exists
- my $outfile = "$dumppath/exonerate_map.$i";
+ my $outfile = "$dump_path/exonerate_map.$i";
push @missing, $outfile unless (-s "$outfile");
# check no errors occurred
@@ -596,19 +596,19 @@ sub parse_exonerate_results {
$self->logger->info("Parsing exonerate results...\n", 0, 'stamped');
# loop over all result files
- my $dumppath = $self->cache->dump_path;
+ my $dump_path = $self->cache->dump_path;
my $num_files = 0;
my $num_lines = 0;
- opendir(DUMPDIR, $dumppath) or
- $self->logger->error("Can't open $dumppath for reading: $!");
+ opendir(DUMPDIR, $dump_path) or
+ $self->logger->error("Can't open $dump_path for reading: $!");
while (defined(my $file = readdir(DUMPDIR))) {
next unless $file =~ /exonerate_map\.\d+/;
$num_files++;
- open(F, '<', "$dumppath/$file");
+ open(F, '<', "$dump_path/$file");
while (<F>) {
$num_lines++;
diff --git a/modules/Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm b/modules/Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm
index fdc18c0de8..b55b30d49c 100644
--- a/modules/Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm
@@ -59,7 +59,7 @@ sub score_genes {
# debug logging
if ($self->logger->loglevel eq 'debug') {
- $matrix->log('gene', $self->conf->param('dumppath'));
+ $matrix->log('gene', $self->conf->param('basedir'));
}
# log stats of combined matrix
@@ -90,7 +90,7 @@ sub scores_from_transcript_scores {
throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
}
- my $dump_path = path_append($self->conf->param('dumppath'), 'matrix');
+ my $dump_path = path_append($self->conf->param('basedir'), 'matrix');
my $matrix = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
-DUMP_PATH => $dump_path,
diff --git a/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper.pm b/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper.pm
index 3941e18c21..bd2fe1b497 100644
--- a/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper.pm
@@ -71,7 +71,7 @@ sub map_genes {
$self->logger->info("== Internal ID mapping for genes...\n\n", 0, 'stamped');
- my $dump_path = path_append($self->conf->param('dumppath'), 'mapping');
+ my $dump_path = path_append($self->conf->param('basedir'), 'mapping');
my $mappings = Bio::EnsEMBL::IdMapping::MappingList->new(
-DUMP_PATH => $dump_path,
@@ -200,7 +200,7 @@ sub map_genes {
$mappings->write_to_file;
if ($self->logger->loglevel eq 'debug') {
- $mappings->log('gene', $self->conf->param('dumppath'));
+ $mappings->log('gene', $self->conf->param('basedir'));
}
$self->logger->info("Done.\n\n", 0, 'stamped');
@@ -235,7 +235,7 @@ sub map_transcripts {
$self->logger->info("== Internal ID mapping for transcripts...\n\n", 0, 'stamped');
- my $dump_path = path_append($self->conf->param('dumppath'), 'mapping');
+ my $dump_path = path_append($self->conf->param('basedir'), 'mapping');
my $mappings = Bio::EnsEMBL::IdMapping::MappingList->new(
-DUMP_PATH => $dump_path,
@@ -358,7 +358,7 @@ sub map_transcripts {
$mappings->write_to_file;
if ($self->logger->loglevel eq 'debug') {
- $mappings->log('transcript');
+ $mappings->log('transcript', $self->conf->param('basedir'));
}
$self->logger->info("Done.\n\n", 0, 'stamped');
@@ -394,7 +394,7 @@ sub map_exons {
$self->logger->info("== Internal ID mapping for exons...\n\n", 0, 'stamped');
- my $dump_path = path_append($self->conf->param('dumppath'), 'mapping');
+ my $dump_path = path_append($self->conf->param('basedir'), 'mapping');
my $mappings = Bio::EnsEMBL::IdMapping::MappingList->new(
-DUMP_PATH => $dump_path,
@@ -463,7 +463,7 @@ sub map_exons {
$mappings->write_to_file;
if ($self->logger->loglevel eq 'debug') {
- $mappings->log('exon');
+ $mappings->log('exon', $self->conf->param('basedir'));
}
$self->logger->info("Done.\n\n", 0, 'stamped');
@@ -487,7 +487,7 @@ sub map_translations {
$self->logger->info("== Internal ID mapping for translations...\n\n", 0, 'stamped');
- my $dump_path = path_append($self->conf->param('dumppath'), 'mapping');
+ my $dump_path = path_append($self->conf->param('basedir'), 'mapping');
my $mappings = Bio::EnsEMBL::IdMapping::MappingList->new(
-DUMP_PATH => $dump_path,
@@ -545,7 +545,7 @@ sub map_translations {
$mappings->write_to_file;
if ($self->logger->loglevel eq 'debug') {
- $mappings->log('translation');
+ $mappings->log('translation', $self->conf->param('basedir'));
}
$self->logger->info("Done.\n\n", 0, 'stamped');
@@ -576,7 +576,7 @@ sub basic_mapping {
# Create a new MappingList object. Specify AUTO_LOAD to load serialised
# existing mappings if found
- my $dump_path = path_append($self->conf->param('dumppath'), 'mapping');
+ my $dump_path = path_append($self->conf->param('basedir'), 'mapping');
my $mappings = Bio::EnsEMBL::IdMapping::MappingList->new(
-DUMP_PATH => $dump_path,
@@ -776,7 +776,7 @@ sub same_gene_transcript_mapping {
# Create a new MappingList object. Specify AUTO_LOAD to load serialised
# existing mappings if found
- my $dump_path = path_append($self->conf->param('dumppath'), 'mapping');
+ my $dump_path = path_append($self->conf->param('basedir'), 'mapping');
my $mappings = Bio::EnsEMBL::IdMapping::MappingList->new(
-DUMP_PATH => $dump_path,
@@ -869,7 +869,7 @@ sub log_ambiguous {
}
# create dump directory if it doesn't exist
- my $debug_path = $self->conf->param('dumppath').'/debug';
+ my $debug_path = $self->conf->param('basedir').'/debug';
unless (-d $debug_path) {
system("mkdir -p $debug_path") == 0 or
throw("Unable to create directory $debug_path.\n");
diff --git a/modules/Bio/EnsEMBL/IdMapping/ResultAnalyser.pm b/modules/Bio/EnsEMBL/IdMapping/ResultAnalyser.pm
index 53702cb27c..9d3fb696af 100644
--- a/modules/Bio/EnsEMBL/IdMapping/ResultAnalyser.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/ResultAnalyser.pm
@@ -462,7 +462,7 @@ sub create_summary_email {
print $fh sprintf($fmt2, qw(DIRECTORY DESCRIPTION));
print $fh ('-'x72), "\n";
- print $fh sprintf($fmt2, 'basedir', $self->conf->param('dumppath'));
+ print $fh sprintf($fmt2, 'basedir', $self->conf->param('basedir'));
foreach my $o (@output) {
print $fh sprintf($fmt2, '$basedir/'.$o->[0], $o->[1]);
diff --git a/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm b/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm
index 9f6733039b..e884d99c6c 100644
--- a/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm
@@ -64,7 +64,7 @@ sub create_shrinked_matrix {
throw('Need a cache file name.') unless ($cache_file);
- my $dump_path = path_append($self->conf->param('dumppath'), 'matrix');
+ my $dump_path = path_append($self->conf->param('basedir'), 'matrix');
$cache_file .= '.ser';
my $shrinked_matrix = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
diff --git a/modules/Bio/EnsEMBL/IdMapping/StableIdMapper.pm b/modules/Bio/EnsEMBL/IdMapping/StableIdMapper.pm
index 091eecc015..b294eae345 100644
--- a/modules/Bio/EnsEMBL/IdMapping/StableIdMapper.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/StableIdMapper.pm
@@ -453,7 +453,7 @@ sub filter_same_gene_transcript_similarities {
# create a new matrix for the filtered entries
my $filtered_scores = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
- -DUMP_PATH => $self->conf->param('dumppath'),
+ -DUMP_PATH => path_append($self->conf->param('basedir'), 'matrix'),
-CACHE_FILE => 'filtered_transcript_scores.ser',
);
@@ -513,7 +513,7 @@ sub generate_translation_similarity_events {
# create a fake translation scoring matrix
my $translation_scores = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
- -DUMP_PATH => $self->conf->param('dumppath'),
+ -DUMP_PATH => path_append($self->conf->param('basedir'), 'matrix'),
-CACHE_FILE => 'translation_scores.ser',
);
diff --git a/modules/Bio/EnsEMBL/IdMapping/SyntenyFramework.pm b/modules/Bio/EnsEMBL/IdMapping/SyntenyFramework.pm
index 2956d019e5..c2e50544d3 100644
--- a/modules/Bio/EnsEMBL/IdMapping/SyntenyFramework.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/SyntenyFramework.pm
@@ -213,7 +213,7 @@ sub rescore_gene_matrix_lsf {
my $num_jobs = $self->conf->param('synteny_rescore_jobs') || 20;
$num_jobs++;
- my $dump_path = path_append($self->conf->param('dumppath'),
+ my $dump_path = path_append($self->conf->param('basedir'),
'matrix/synteny_rescore');
$self->logger->debug("Creating sub-matrices...\n", 0, 'stamped');
@@ -376,7 +376,7 @@ sub logger {
Arg[1] : (optional) Bio::EnsEMBL::Utils::ConfParser - the configuration
to set
- Example : my $dumppath = $object->conf->param('dumppath');
+ Example : my $basedir = $object->conf->param('basedir');
Description : Getter/setter for configuration object
Return type : Bio::EnsEMBL::Utils::ConfParser
Exceptions : none
diff --git a/modules/Bio/EnsEMBL/IdMapping/TranscriptScoreBuilder.pm b/modules/Bio/EnsEMBL/IdMapping/TranscriptScoreBuilder.pm
index ea6591c15b..7d2ee79a7f 100644
--- a/modules/Bio/EnsEMBL/IdMapping/TranscriptScoreBuilder.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/TranscriptScoreBuilder.pm
@@ -59,7 +59,7 @@ sub score_transcripts {
# debug logging
if ($self->logger->loglevel eq 'debug') {
- $matrix->log('transcript', $self->conf->param('dumppath'));
+ $matrix->log('transcript', $self->conf->param('basedir'));
}
# log stats of combined matrix
@@ -90,7 +90,7 @@ sub scores_from_exon_scores {
throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
}
- my $dump_path = path_append($self->conf->param('dumppath'), 'matrix');
+ my $dump_path = path_append($self->conf->param('basedir'), 'matrix');
my $matrix = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
-DUMP_PATH => $dump_path,
--
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