Trees | Indices | Help |
---|
|
Module containing different tools for sequence motif analysis.
it contains the core Motif class containing various I/O methods as well as methods for motif comparisons and motif searching in sequences. It also inlcudes functionality for parsing AlignACE and MEME programs
|
|||
|
|
|||
|
|||
|
|||
|
|||
|
|||
|
|
|||
_parsers = {"AlignAce": AlignAceParser, "MEME": MEMEParser}
|
|||
_readers = {"jaspar-pfm": _from_pfm, "jaspar-sites": _from_sites}
|
|||
__package__ =
|
|
Parses an output file of motif finding programs. Currently supported formats:
You can also use single-motif formats, although the Bio.Motif.read() function is simpler to use in this situation.
For example: >>> from Bio import Motif >>> for motif in Motif.parse(open("Motif/alignace.out"),"AlignAce"): ... print motif.consensus() TCTACGATTGAG CTGCACCTAGCTACGAGTGAG GTGCCCTAAGCATACTAGGCG GCCACTAGCAGAGCAGGGGGC CGACTCAGAGGTT CCACGCTAAGAGAAGTGCCGGAG GCACGTCCCTGAGCA GTCCATCGCAAAGCGTGGGGC GAGATCAGAGGGCCG TGGACGCGGGG GACCAGAGCCTCGCATGGGGG AGCGCGCGTG GCCGGTTGCTGTTCATTAGG ACCGACGGCAGCTAAAAGGG GACGCCGGGGAT CGACTCGCGCTTACAAGG |
Reads a motif from a handle using a specified file-format. This supports the same formats as Bio.Motif.parse(), but only for files containing exactly one record. For example, reading a pfm file: >>> from Bio import Motif >>> motif = Motif.read(open("Motif/SRF.pfm"),"jaspar-pfm") >>> motif.consensus() Seq('GCCCATATATGG', IUPACUnambiguousDNA()) Or a single-motif MEME file, >>> from Bio import Motif >>> motif = Motif.read(open("Motif/meme.out"),"MEME") >>> motif.consensus() Seq('CTCAATCGTA', IUPACUnambiguousDNA()) If the handle contains no records, or more than one record, an exception is raised: >>> from Bio import Motif >>> motif = Motif.read(open("Motif/alignace.out"),"AlignAce") Traceback (most recent call last): ... ValueError: More than one motif found in handle If however you want the first record from a file containing multiple records this function would raise an exception (as shown in the example above). Instead use: >>> from Bio import Motif >>> motif = Motif.parse(open("Motif/alignace.out"),"AlignAce").next() >>> motif.consensus() Seq('TCTACGATTGAG', IUPACUnambiguousDNA()) Use the Bio.Motif.parse(handle, format) function if you want to read multiple records from the handle. |
Run the Bio.Motif module's doctests. This will try and locate the unit tests directory, and run the doctests from there in order that the relative paths used in the examples work. |
Trees | Indices | Help |
---|
Generated by Epydoc 3.0.1 on Wed Jul 14 01:49:22 2010 | http://epydoc.sourceforge.net |