log << counter.to_s + ': ' + phylogeny_file + ' -> ' + outfile + NL
phylogeny_id = get_id( phylogeny_file )
-
+ puts "id:" + phylogeny_id
+
ids_mapfile_name = nil
domains_mapfile_name = nil
seqs_file_name = nil
def get_id( phylogeny_file_name )
- phylogeny_file_name =~ /^([^_]+)/
+ phylogeny_file_name =~ /^(.+?)__/
$1
end
def get_file( files_in_dir, phylogeny_id, suffix_pattern )
matching_files = Array.new
- matching_suffix_files = Array.new
+
files_in_dir.each { | file |
if ( !File.directory?( file ) &&
file !~ /^\./ &&
file !~ /^00/ &&
- file =~ /^#{phylogeny_id}.*#{suffix_pattern}$/ )
+ 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 +
'_] [' + suffix_pattern + '] present in current directory' )
end
file =~ /^#{phylogeny_id}.+\d$/ )
matching_files << file
end
-
}
if matching_files.length < 1