| Previous changeset 17:3eada762af11 (2018-10-23) Next changeset 19:db2480de852e (2020-08-21) |
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Commit message:
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 960f4708be7cdd486e4569e7b44eb856b2cad79d-dirty |
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modified:
blast.py |
| b |
| diff -r 3eada762af11 -r 1250aab8b97a blast.py --- a/blast.py Tue Oct 23 06:24:33 2018 -0400 +++ b/blast.py Fri Feb 22 09:54:46 2019 -0500 |
| [ |
| b'@@ -13,10 +13,12 @@\n log = logging.getLogger(__name__)\n \n # Note implicit string concatenation here to avoid excessively long lines:\n-_DOCTYPES = [\'<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" \'\n- \'"http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\',\n- \'<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" \'\n- \'"NCBI_BlastOutput.dtd">\']\n+_DOCTYPES = [\n+ \'<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" \'\n+ \'"http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\',\n+ \'<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" \'\n+ \'"NCBI_BlastOutput.dtd">\',\n+]\n \n \n class BlastXml(GenericXml):\n@@ -28,10 +30,10 @@\n """Set the peek and blurb text."""\n if not dataset.dataset.purged:\n dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)\n- dataset.blurb = \'NCBI Blast XML data\'\n+ dataset.blurb = "NCBI Blast XML data"\n else:\n- dataset.peek = \'file does not exist\'\n- dataset.blurb = \'file purged from disk\'\n+ dataset.peek = "file does not exist"\n+ dataset.blurb = "file purged from disk"\n \n def sniff(self, filename):\n """Determine from the contents if the file is blastxml.\n@@ -58,7 +60,7 @@\n handle.close()\n return False\n line = handle.readline()\n- if line.strip() != \'<BlastOutput>\':\n+ if line.strip() != "<BlastOutput>":\n handle.close()\n return False\n handle.close()\n@@ -74,8 +76,10 @@\n # For one file only, use base class method (move/copy)\n return Text.merge(split_files, output_file)\n if not split_files:\n- raise ValueError("Given no BLAST XML files, %r, to merge into %s"\n- % (split_files, output_file))\n+ raise ValueError(\n+ "Given no BLAST XML files, %r, to merge into %s"\n+ % (split_files, output_file)\n+ )\n out = open(output_file, "w")\n h = None\n for f in split_files:\n@@ -138,20 +142,25 @@\n # Enough to check <BlastOutput_program> and <BlastOutput_version> match\n out.close()\n h.close()\n- raise ValueError("BLAST XML headers don\'t match for %s and %s - have:\\n%s\\n...\\n\\nAnd:\\n%s\\n...\\n"\n- % (split_files[0], f, old_header[:300], header[:300]))\n+ raise ValueError(\n+ "BLAST XML headers don\'t match for %s and %s - have:\\n"\n+ "%s\\n...\\n\\nAnd:\\n%s\\n...\\n"\n+ % (split_files[0], f, old_header[:300], header[:300])\n+ )\n else:\n out.write(" <Iteration>\\n")\n for line in h:\n if "</BlastOutput_iterations>" in line:\n break\n- # TODO - Increment <Iteration_iter-num> and if required automatic query names\n- # like <Iteration_query-ID>Query_3</Iteration_query-ID> to be increasing?\n+ # TODO - Increment <Iteration_iter-num> and if required automatic query\n+ # names like <Iteration_query-ID>Query_3</Iteration_query-ID> to be\n+ # increasing?\n out.write(line)\n h.close()\n out.write(" </BlastOutput_iterations>\\n")\n out.write("</BlastOutput>\\n")\n out.close()\n+\n merge = staticmethod(merge)\n \n \n@@ -164,8 +173,8 @@\n dataset.peek = "BLAST database (multiple files)"\n dataset.blurb = "BLAST database (multiple files)"\n else:\n- dataset.peek = \'file does not exist\'\n- dataset.blurb = \'file purged from disk\'\n+ dataset.peek = "file does not exist"\n+ dataset.blurb = "file purged from disk"\n \n def display_peek(self, dataset):\n """Create HTML content, used for displaying peek'..b' # self.add_composite_file(\'blastdb.00.idx\', is_binary=True, optional=True)\n@@ -279,24 +307,24 @@\n class BlastProtDb(_BlastDb, Data):\n """Class for protein BLAST database files."""\n \n- file_ext = \'blastdbp\'\n+ file_ext = "blastdbp"\n allow_datatype_change = False\n- composite_type = \'basic\'\n+ composite_type = "basic"\n \n def __init__(self, **kwd):\n """Initialize the class."""\n Data.__init__(self, **kwd)\n # Component file comments are as in BlastNucDb except where noted\n- self.add_composite_file(\'blastdb.phr\', is_binary=True)\n- self.add_composite_file(\'blastdb.pin\', is_binary=True)\n- self.add_composite_file(\'blastdb.psq\', is_binary=True) # protein sequences\n- self.add_composite_file(\'blastdb.phd\', is_binary=True, optional=True)\n- self.add_composite_file(\'blastdb.phi\', is_binary=True, optional=True)\n- self.add_composite_file(\'blastdb.pnd\', is_binary=True, optional=True)\n- self.add_composite_file(\'blastdb.pni\', is_binary=True, optional=True)\n- self.add_composite_file(\'blastdb.pog\', is_binary=True, optional=True)\n- self.add_composite_file(\'blastdb.psd\', is_binary=True, optional=True)\n- self.add_composite_file(\'blastdb.psi\', is_binary=True, optional=True)\n+ self.add_composite_file("blastdb.phr", is_binary=True)\n+ self.add_composite_file("blastdb.pin", is_binary=True)\n+ self.add_composite_file("blastdb.psq", is_binary=True) # protein sequences\n+ self.add_composite_file("blastdb.phd", is_binary=True, optional=True)\n+ self.add_composite_file("blastdb.phi", is_binary=True, optional=True)\n+ self.add_composite_file("blastdb.pnd", is_binary=True, optional=True)\n+ self.add_composite_file("blastdb.pni", is_binary=True, optional=True)\n+ self.add_composite_file("blastdb.pog", is_binary=True, optional=True)\n+ self.add_composite_file("blastdb.psd", is_binary=True, optional=True)\n+ self.add_composite_file("blastdb.psi", is_binary=True, optional=True)\n # self.add_composite_file(\'blastdb.paa\', is_binary=True, optional=True)\n # self.add_composite_file(\'blastdb.pab\', is_binary=True, optional=True)\n # self.add_composite_file(\'blastdb.pac\', is_binary=True, optional=True)\n@@ -307,19 +335,19 @@\n class BlastDomainDb(_BlastDb, Data):\n """Class for domain BLAST database files."""\n \n- file_ext = \'blastdbd\'\n+ file_ext = "blastdbd"\n allow_datatype_change = False\n- composite_type = \'basic\'\n+ composite_type = "basic"\n \n def __init__(self, **kwd):\n """Initialize the class."""\n Data.__init__(self, **kwd)\n- self.add_composite_file(\'blastdb.phr\', is_binary=True)\n- self.add_composite_file(\'blastdb.pin\', is_binary=True)\n- self.add_composite_file(\'blastdb.psq\', is_binary=True)\n- self.add_composite_file(\'blastdb.freq\', is_binary=True, optional=True)\n- self.add_composite_file(\'blastdb.loo\', is_binary=True, optional=True)\n- self.add_composite_file(\'blastdb.psd\', is_binary=True, optional=True)\n- self.add_composite_file(\'blastdb.psi\', is_binary=True, optional=True)\n- self.add_composite_file(\'blastdb.rps\', is_binary=True, optional=True)\n- self.add_composite_file(\'blastdb.aux\', is_binary=True, optional=True)\n+ self.add_composite_file("blastdb.phr", is_binary=True)\n+ self.add_composite_file("blastdb.pin", is_binary=True)\n+ self.add_composite_file("blastdb.psq", is_binary=True)\n+ self.add_composite_file("blastdb.freq", is_binary=True, optional=True)\n+ self.add_composite_file("blastdb.loo", is_binary=True, optional=True)\n+ self.add_composite_file("blastdb.psd", is_binary=True, optional=True)\n+ self.add_composite_file("blastdb.psi", is_binary=True, optional=True)\n+ self.add_composite_file("blastdb.rps", is_binary=True, optional=True)\n+ self.add_composite_file("blastdb.aux", is_binary=True, optional=True)\n' |