cls.GAFReader.CGAFReader Class Reference

Collaboration diagram for cls.GAFReader.CGAFReader:

Public Member Functions
def	__init__ (s)
def	Read (s, ffn, ac)
	Reads in an GO annotation file and stores its (filtered) content into an annotation corpus. More...
def	SetFilter (s, which=GAF_FILTER_NONE)
	Set a filter group by its token. More...
def	SetFilterCodes (s, codes=GAF_FILTER_NONE)
	Set the list of accepted evidence codes. More...
def	plot (graph, ffn)

Static Public Attributes
list	apo
string	base = "/Users/chris/progs/dint/data/go/";
string	goaffn = base + "treetest.goa.tsv";
string	graphffn = base + "treetest.graphml";
	g = ig.load(graphffn);
	bp = CAnnotationCorpus("biological_process");
	r = CGAFReader();

Constructor & Destructor Documentation

__init__()

def cls.GAFReader.CGAFReader.__init__

(

s

)

Member Function Documentation

plot()

def cls.GAFReader.CGAFReader.plot	(		graph,
			ffn
	)

Read()

def cls.GAFReader.CGAFReader.Read	(		s,
			ffn,
			ac
	)

Reads in an GO annotation file and stores its (filtered) content into an annotation corpus.

Parameters

ffn	Full file name of the GOA file. @parma ac Instance of cls.AnnotationCorpus.AnnotationCorpus.

Returns

True, everything ok; False, problem with the file, an error message has been issued.

SetFilter()

def cls.GAFReader.CGAFReader.SetFilter	(		s,
			which = GAF_FILTER_NONE
	)

Set a filter group by its token.

    @param which  Any of the @c GAF_* tokens defined at the beginning. If
    the parameter is left to @c None, filtering is skipped and all
    annotations are read.

SetFilterCodes()

def cls.GAFReader.CGAFReader.SetFilterCodes	(		s,
			codes = GAF_FILTER_NONE
	)

Set the list of accepted evidence codes.

    @param codes  (@c List, @c Tuple) Evidence code @c Strings that are
    accepted by the reader. Annotations with codes that are not in this
    list are rejected. If parameter is left to @c None, the filtering is
    stopped and everything is read. Evidence codes are not checked for
    compliance with GO definitions.
    @return @c True, all went ok. @c False, supply of improper codes. No
    filtering is done.

Member Data Documentation

apo

list cls.GAFReader.CGAFReader.apo

static

Initial value:

=  ["GO:0008150","GO:0065007", "GO:0009987", "GO:0044699",
           "GO:0016265", "GO:0050789", "GO:0044763", "GO:0008219",
           "GO:0050794", "GO:0050896", "GO:0023052", "GO:0007154",
           "GO:0051716", "GO:0048518", "GO:0012501", "GO:0010941",
           "GO:0044700", "GO:0006915", "GO:0048522", "GO:0010646",
           "GO:0043067", "GO:0048583", "GO:0023051", "GO:0007165",
           "GO:0097190", "GO:0007166", "GO:0010647", "GO:0048584",
           "GO:0023056", "GO:0042981", "GO:0009966", "GO:0097191",
           "GO:0009967", "GO:2001233", "GO:0038034", "GO:0097192",
           "GO:2001235", "GO:2001236", "GO:2001238", "GO:2001239",
           "GO:2001241"];

base

string cls.GAFReader.CGAFReader.base = "/Users/chris/progs/dint/data/go/";

static

bp

cls.GAFReader.CGAFReader.bp = CAnnotationCorpus("biological_process");

static

g

cls.GAFReader.CGAFReader.g = ig.load(graphffn);

static

goaffn

string cls.GAFReader.CGAFReader.goaffn = base + "treetest.goa.tsv";

static

graphffn

string cls.GAFReader.CGAFReader.graphffn = base + "treetest.graphml";

static

r

cls.GAFReader.CGAFReader.r = CGAFReader();

static

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The documentation for this class was generated from the following file:

• cls/GAFReader.py