changeset 13:cd6c4bd14718

Uploaded

--- 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",