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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
85e2478
..
1eea808
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"
@@
-166,6
+166,12
@@
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 )
+ 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
ids_mapfile_name = nil
domains_mapfile_name = nil
@@
-175,7
+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
@@
-195,22
+200,34
@@
module Evoruby
end
cmd = decorator +
end
cmd = decorator +
- ' -p -f=m ' + phylogeny_file + ' ' +
+ ' -t -p -f=m ' + phylogeny_file + ' ' +
seqs_file_name + ' ' + TMP_FILE_1
puts cmd
seqs_file_name + ' ' + TMP_FILE_1
puts cmd
- execute_cmd( cmd, log )
+ begin
+ execute_cmd( cmd, log )
+ rescue Error
+ Util.fatal_error( PRG_NAME, 'error: ' + $! )
+ end
cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
'-f=d ' + TMP_FILE_1 + ' ' +
domains_mapfile_name + ' ' +TMP_FILE_2
puts cmd
cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
'-f=d ' + TMP_FILE_1 + ' ' +
domains_mapfile_name + ' ' +TMP_FILE_2
puts cmd
- execute_cmd( cmd, log )
+ begin
+ execute_cmd( cmd, log )
+ rescue Error
+ Util.fatal_error( PRG_NAME, 'error: ' + $! )
+ end
cmd = decorator + ' ' + DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
'-f=n ' + TMP_FILE_2 + ' ' +
ids_mapfile_name + ' ' + outfile
puts cmd
cmd = decorator + ' ' + DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
'-f=n ' + TMP_FILE_2 + ' ' +
ids_mapfile_name + ' ' + outfile
puts cmd
- execute_cmd( cmd, log )
+ begin
+ execute_cmd( cmd, log )
+ rescue Error
+ Util.fatal_error( PRG_NAME, 'error: ' + $! )
+ end
File.delete( TMP_FILE_1 )
File.delete( TMP_FILE_2 )
File.delete( TMP_FILE_1 )
File.delete( TMP_FILE_2 )
@@
-236,13
+253,17
@@
module Evoruby
def get_id( phylogeny_file_name )
def get_id( phylogeny_file_name )
- phylogeny_file_name =~ /^([^_]+)/
- $1
+ if phylogeny_file_name =~ /^(.+?)__/
+ return $1
+ elsif phylogeny_file_name =~ /^(.+?)_/
+ return $1
+ end
+ nil
end
def get_file( files_in_dir, phylogeny_id, suffix_pattern )
matching_files = Array.new
end
def get_file( files_in_dir, phylogeny_id, suffix_pattern )
matching_files = Array.new
- matching_suffix_files = Array.new
+
files_in_dir.each { | file |
if ( !File.directory?( file ) &&
files_in_dir.each { | file |
if ( !File.directory?( file ) &&
@@
-251,24
+272,14
@@
module Evoruby
file =~ /^#{phylogeny_id}.*#{suffix_pattern}$/ )
matching_files << file
end
file =~ /^#{phylogeny_id}.*#{suffix_pattern}$/ )
matching_files << file
end
- if ( !File.directory?( file ) &&
- file !~ /^\./ &&
- file !~ /^00/ &&
- file =~ /#{suffix_pattern}$/ )
- matching_suffix_files << file
- end
}
}
- if matching_files.length < 1 && matching_suffix_files.length == 1
- return matching_suffix_files[ 0 ]
- end
-
- if matching_files.length < 1 && matching_suffix_files.length < 1
+ if matching_files.length < 1
Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id +
Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id +
- '_] [' + suffix_pattern + '] present in current directory' )
+ '...' + 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
@@
-281,17
+292,18
@@
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
matching_files << file
end
-
}
if matching_files.length < 1
}
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