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[jalview.git]
/
forester
/
ruby
/
evoruby
/
lib
/
evo
/
tool
/
phylogenies_decorator.rb
diff --git
a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
index
b2d5a87
..
52c94e0
100644
(file)
--- a/
forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
+++ b/
forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
@@
-30,8
+30,8
@@
module Evoruby
#DECORATOR_OPTIONS_DOMAINS = '-r=1'
DECORATOR_OPTIONS_DOMAINS = '-p -t'
IDS_MAPFILE_SUFFIX = '.nim'
#DECORATOR_OPTIONS_DOMAINS = '-r=1'
DECORATOR_OPTIONS_DOMAINS = '-p -t'
IDS_MAPFILE_SUFFIX = '.nim'
- DOMAINS_MAPFILE_SUFFIX = '.dff'
- SLEEP_TIME = 0.1
+ DOMAINS_MAPFILE_SUFFIX = '_hmmscan_10.dff'
+ SLEEP_TIME = 0.05
REMOVE_NI = true
TMP_FILE_1 = '___PD1___'
TMP_FILE_2 = '___PD2___'
REMOVE_NI = true
TMP_FILE_1 = '___PD1___'
TMP_FILE_2 = '___PD2___'
@@
-40,10
+40,10
@@
module Evoruby
JAVA_HOME = ENV[Constants::JAVA_HOME_ENV_VARIABLE]
PRG_NAME = "phylogenies_decorator"
JAVA_HOME = ENV[Constants::JAVA_HOME_ENV_VARIABLE]
PRG_NAME = "phylogenies_decorator"
- PRG_DATE = "2012.10.11"
+ PRG_DATE = "2013.11.15"
PRG_DESC = "decoration of phylogenies with sequence/species names and domain architectures"
PRG_VERSION = "1.02"
PRG_DESC = "decoration of phylogenies with sequence/species names and domain architectures"
PRG_VERSION = "1.02"
- COPYRIGHT = "2012 Christian M Zmasek"
+ COPYRIGHT = "2013 Christian M Zmasek"
CONTACT = "phylosoft@gmail.com"
WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"
CONTACT = "phylosoft@gmail.com"
WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"
@@
-166,8
+166,13
@@
module Evoruby
log << counter.to_s + ': ' + phylogeny_file + ' -> ' + outfile + NL
phylogeny_id = get_id( phylogeny_file )
log << counter.to_s + ': ' + phylogeny_file + ' -> ' + outfile + NL
phylogeny_id = get_id( phylogeny_file )
- puts "id:" + phylogeny_id
-
+ if phylogeny_id == nil || phylogeny_id.size < 1
+ Util.fatal_error( PRG_NAME, 'could not get id from ' + phylogeny_file.to_s )
+ end
+ puts
+ Util.print_message( PRG_NAME, "id: " + phylogeny_id )
+ log << "id: " + phylogeny_id + NL
+
ids_mapfile_name = nil
domains_mapfile_name = nil
seqs_file_name = nil
ids_mapfile_name = nil
domains_mapfile_name = nil
seqs_file_name = nil
@@
-176,7
+181,6
@@
module Evoruby
domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX )
seqs_file_name = get_seq_file( files, phylogeny_id )
domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX )
seqs_file_name = get_seq_file( files, phylogeny_id )
-
begin
Util.check_file_for_readability( domains_mapfile_name )
rescue ArgumentError
begin
Util.check_file_for_readability( domains_mapfile_name )
rescue ArgumentError
@@
-243,7
+247,7
@@
module Evoruby
def get_file( files_in_dir, phylogeny_id, suffix_pattern )
matching_files = Array.new
def get_file( files_in_dir, phylogeny_id, suffix_pattern )
matching_files = Array.new
-
+
files_in_dir.each { | file |
if ( !File.directory?( file ) &&
files_in_dir.each { | file |
if ( !File.directory?( file ) &&
@@
-253,15
+257,13
@@
module Evoruby
matching_files << file
end
}
matching_files << file
end
}
-
-
if matching_files.length < 1
if matching_files.length < 1
- Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id +
- '_] [' + suffix_pattern + '] present in current directory' )
+ Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id
+ + suffix_pattern + '] present in current directory' )
end
if matching_files.length > 1
end
if matching_files.length > 1
- Util.fatal_error( PRG_NAME, 'more than one file matching [' + phylogeny_id +
- '_] [' + suffix_pattern + '] present in current directory' )
+ Util.fatal_error( PRG_NAME, 'more than one file matching [' + phylogeny_id
+ + suffix_pattern + '] present in current directory' )
end
matching_files[ 0 ]
end
end
matching_files[ 0 ]
end
@@
-274,16
+276,16
@@
module Evoruby
if ( !File.directory?( file ) &&
file !~ /^\./ &&
file !~ /^00/ &&
if ( !File.directory?( file ) &&
file !~ /^\./ &&
file !~ /^00/ &&
- file =~ /^#{phylogeny_id}.+\d$/ )
+ ( file =~ /^#{phylogeny_id}__.+\d$/ || file =~ /^#{phylogeny_id}__.*\.fasta$/ ) )
matching_files << file
end
}
if matching_files.length < 1
matching_files << file
end
}
if matching_files.length < 1
- Util.fatal_error( PRG_NAME, 'no seq file matching [' + phylogeny_id + '] present in current directory' )
+ Util.fatal_error( PRG_NAME, 'no seq file matching [' + phylogeny_id + '__] present in current directory' )
end
if matching_files.length > 1
end
if matching_files.length > 1
- Util.fatal_error( PRG_NAME, 'more than one seq file matching [' + phylogeny_id + '] present in current directory' )
+ Util.fatal_error( PRG_NAME, 'more than one seq file matching [' + phylogeny_id + '__] present in current directory' )
end
matching_files[ 0 ]
end
end
matching_files[ 0 ]
end