biopython/biopython — pull request #175 by bow (2013-04-06 21:36:25+00:00)
Title: Update SearchIO to support new BLAST 2.2.28+ additions

The [recently released](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/) BLAST 2.2.28+ brings in new columns for its tabular format.

This pull request updates the SearchIO blast tabular parser to support parsing and writing these new columns. Some column values which are basically lists (';'-separated strings) are also parsed into Python lists now. They're restored to strings again upon writing to a file. Finally, I also found a bug in the blast-tab writer where the whole SeqRecord is written (instead of its sequence only). This has been fixed and we now have an additional test to check for this behavior.