| Previous changeset 12:b819394a2634 (2012-02-22) Next changeset 14:778f03497adb (2012-02-24) |
|
Commit message:
Uploaded |
|
modified:
weblogolib/__init__.py |
| b |
| diff -r b819394a2634 -r cd6c4bd14718 weblogolib/__init__.py --- a/weblogolib/__init__.py Wed Feb 22 06:42:17 2012 -0500 +++ b/weblogolib/__init__.py Fri Feb 24 09:26:11 2012 -0500 |
| [ |
| @@ -981,7 +981,7 @@ if weight is None and alphabet is not None: weight = float(len(alphabet)) if comp.lower() == 'equiprobable' : prior = weight * equiprobable_distribution(len(alphabet)) - + return prior elif comp.lower() == 'escherichiacoli' : if(altype=="codonsT"): composition="{'CTT': 0.7616, 'ATG': 1.5872, 'ACA': 0.4096, 'ACG': 0.736, 'ATC': 1.1648, 'AAC': 1.5615999999999999, 'ATA': 0.2368, 'AGG': 0.1024, 'CCT': 0.5376000000000001, 'ACT': 0.512, 'AGC': 1.0624, 'AAG': 0.7744, 'AGA': 0.0896, 'CAT': 1.0112, 'AAT': 1.4016, 'ATT': 1.952, 'CTG': 3.0016, 'CTA': 0.3392, 'CTC': 0.672, 'CAC': 0.8383999999999999, 'AAA': 2.1248, 'CCG': 1.7087999999999999, 'AGT': 0.4608, 'CCA': 0.4224, 'CAA': 0.7744, 'CCC': 0.4096, 'TAT': 1.0752000000000002, 'GGT': 1.3632, 'TGT': 0.37760000000000005, 'CGA': 0.2752, 'CAG': 1.7728, 'TCT': 0.3648, 'GAT': 2.4255999999999998, 'CGG': 0.26239999999999997, 'TTT': 1.2608, 'TGC': 0.512, 'GGG': 0.5504, 'TAG': 1e-06, 'GGA': 0.5888, 'TAA': 0.1152, 'GGC': 2.1376, 'TAC': 0.9344, 'TTC': 0.96, 'TCG': 0.512, 'TTA': 0.9728, 'TTG': 0.7616, 'TCC': 0.352, 'ACC': 1.4592, 'TCA': 0.4992, 'GCA': 1.3504, 'GTA': 0.736, 'GCC': 2.0224, 'GTC': 0.7487999999999999, 'GCG': 2.464, 'GTG': 1.6896, 'GAG': 1.1776, 'GTT': 1.0752000000000002, 'GCT': 0.6848, 'TGA': 0.064, 'GAC': 1.312, 'CGT': 1.3504, 'TGG': 0.6848, 'GAA': 2.7968, 'CGC': 1.664}" @@ -1004,13 +1004,13 @@ prior = weight * equiprobable_distribution(len(alphabet)) elif comp in std_percentCG : prior = weight * base_distribution(std_percentCG[comp]) - + return prior elif comp[-1] == '%' : prior = weight * base_distribution( float(comp[:-1])) - + return prior elif isfloat(comp) : prior = weight * base_distribution( float(comp)*100. ) - + return prior if composition[0] == '{' and composition[-1] == '}' : explicit = composition[1: -1] explicit = explicit.replace(',',' ').replace("'", ' ').replace('"',' ').replace(':', ' ').split() @@ -1646,8 +1646,8 @@ dest="composition", action="store", type="string", - default = "auto", - help="The expected composition of the sequences: 'auto' (default), 'equiprobable', 'none' (Do not perform any compositional adjustment), or 'escherichiacoli' 'homosapiens' 'saccharomycescerevisiae' for ecoli, human and SC codon frequencies.", + default = "equiprobable", + help="The expected composition of the sequences: 'equiprobable'(default), 'none' (Do not perform any compositional adjustment), or 'escherichiacoli' 'homosapiens' 'saccharomycescerevisiae' for ecoli, human and SC codon frequencies.", metavar="COMP.") data_grp.add_option( "", "--weight", |