@@ -9,6 +9,16 @@ It also includes a very simple interface to CompareACE tool. http://atlas.med.harvard.edu/ Now superseded by Bio.Motif + +Class mapping: +Bio.AlignAce.AlignAceStandalone -> Bio.Motif.Applications.AlignAceCommandline +Bio.AlignAce.CompareAceStandalone -> Bio.Motif.Applications.CompareAceCommandline +Bio.Alignace.Motif -> Bio.Motif.Motif +Bio.AlignAce.Parser.CompareAceParser -> Bio.Motif.CompareAceParser + +Instead of using Bio.AlignAce.Parser.AlignAceParser class, you can use +Bio.Motif.parse(handle,format="AlignAce") + """ import warnings Bio/AlignAce/__init__.py @@ -6,6 +6,15 @@ Parser for dealing with text output from the MEME motif search program (DEPRECATED). Now superseded by Bio.Motif + +Class mapping: +Bio.MEME.Motif.MEMEMotif -> Bio.Motif.Motif +Bio.MEME.parser.MEMEParser -> Bio.Motif.MEMEParser +Bio.MEME.parser.MASTParser -> Bio.Motif.MASTParser + +Instead of using Bio.MEME.parser.MEMEParser class, you can use +Bio.Motif.parse(handle,format="MEME") + """ import warnings Bio/MEME/__init__.py @@ -5,3 +5,4 @@ # as part of this package. """Motif command line tool wrappers.""" from _AlignAce import AlignAceCommandline +from _AlignAce import CompareAceCommandline Bio/Motif/Applications/__init__.py @@ -15,7 +15,7 @@ from Parsers.MEME import MEMEParser,MASTParser from Thresholds import ScoreDistribution _parsers={"AlignAce":AlignAceParser, - "MEME":MEMEParser, + "MEME":MEMEParser } def _from_pfm(handle): Bio/Motif/__init__.py c2350f3fd0d18ea593fc9559869448d5133ba2f4 bartek bartek http://github.com/etal/biopython/commit/f0130eec3b65297413e68d20b8d98dc621f9a42c f0130eec3b65297413e68d20b8d98dc621f9a42c 2009-08-21T02:12:16-07:00 2009-08-21T02:12:16-07:00 Info on migrating from Bio.AlignAce and Bio.MEME to Bio.Motif bfa7518060ddd6482378b4cdae44e4b884a4a570 bartek bartek