SGD.py -- Routines for convenient access to SGD data, including cevivsiae genome sequence.
 
 
Copyright (2005) Whitehead Institute for Biomedical Research (except as noted below)
All Rights Reserved
 
Author: David Benjamin Gordon

Modules
		TAMO.seq.Fasta TAMO math pickle re sys

Classes
		featureline   class featureline       Methods defined here: __init__(self, name, alts, ftype, chr, start, stop, desc) __repr__(self)

Functions
		chr_len(number) dist_from_cen(chr, start, stop) dist_from_tel(chr, start, stop) experiment2gene(experiment) experiment2orf(experiment) experiment2swp(experiment) feature(featurename) feature_dist(Astart, Astop, Bstart, Bstop) feature_pos(_feature) featuredict(featuretype) gene2orf(gene_query) gene2pseq(gene) gene2swp(gene) geneabundance(gene) genelocalization(gene) genenonnuclear(gene) get_seq(chr, start=None, stop=None) get_swp_sequence(query) load_localization() load_localization_Kumar() orf2gene(orf_query) orf2other(qorf, qtype) orf2pseq(orf) orf2swp(orf_query) orfabundance(orf) orflocalization(orf) orfnonnuclear(orf) swp2swp(swp) Converts, when possible, from P014543 to ADR1_YEAST swp_find_and_format(swp)

Data
		ChrD = {} SGDdir = '/etc/TAMOdata/SGD/' special_cases = {'BYE1': 'YKL005C', 'GRF10(Pho2)': 'PHO2', 'HDT80': 'NDT80', 'MATA1': 'HMRA1', 'MATa1': 'HMRA1', 'MIG3': 'YER028C', 'NNF2': 'YGR089W', 'SIG1': 'MOT2', 'USV1': 'YPL230W', 'YAP8': 'ARR1'}