in HMMER report becomes '-' instead of digits according to the alignment.
* changes in 1.2 -> 1.3 (sorry, I forgot to write) * using thread to read stderr
* Using block with Open3.popen3 * removed rescue
* constant FASTACMD is changed to an instance variable * added accessors for database and fastacmd * get_by_ids method is integrated into fetch method * test code modified to accept arguments
* Added Bio::SPTR#synomyms method (proposed by Luca Pireddu). * Changed Bio::SPTR#gn to parsing newly GN line format (proposed by Luca Pireddu). * Changed Bio::SPTR#gene_names method (proposed by Luca Pireddu). * Changed Bio::SPTR#gene_name method (proposed by Luca Pireddu).
* clean up
Newly added bl2seq (BLAST 2 sequences) output parser. * lib/bio/appl/blast/format0.rb: Added `self.class::` before F0dbstat.new for bl2seq/report.rb
…method in initialize
…a module and this module is included and extended to make methods as both of instance methods and extend methods * Bio::Sequence::NA class is rewrited (molecular_weight, to_re methods) to use Bio::NucleicAcid * molecular_weight method is fixed to subtract two hydrogens for each base
when parsing features of ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/ Salmonella_typhimurium_LT2/AE006468.gbk