Mercurial > repos > davidmurphy > codonlogo
comparison weblogolib/__init__.py @ 14:778f03497adb
Uploaded
author | davidmurphy |
---|---|
date | Fri, 24 Feb 2012 11:37:26 -0500 |
parents | cd6c4bd14718 |
children |
comparison
equal
deleted
inserted
replaced
13:cd6c4bd14718 | 14:778f03497adb |
---|---|
978 | 978 |
979 if comp.lower() == 'none': return None | 979 if comp.lower() == 'none': return None |
980 | 980 |
981 if weight is None and alphabet is not None: weight = float(len(alphabet)) | 981 if weight is None and alphabet is not None: weight = float(len(alphabet)) |
982 if comp.lower() == 'equiprobable' : | 982 if comp.lower() == 'equiprobable' : |
983 prior = weight * equiprobable_distribution(len(alphabet)) | 983 prior = weight * equiprobable_distribution(len(alphabet)) |
984 return prior | 984 return prior |
985 elif comp.lower() == 'escherichiacoli' : | 985 |
986 if comp.lower() == 'escherichiacoli' : | |
986 if(altype=="codonsT"): | 987 if(altype=="codonsT"): |
987 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}" | 988 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}" |
988 else: | 989 else: |
989 composition="{'CUU': 0.7616, 'AUG': 1.5872, 'ACA': 0.4096, 'ACG': 0.736, 'AUC': 1.1648, 'AAC': 1.5615999999999999, 'AUA': 0.2368, 'AGG': 0.1024, 'CCU': 0.5376000000000001, 'ACU': 0.512, 'AGC': 1.0624, 'AAG': 0.7744, 'AGA': 0.0896, 'CAU': 1.0112, 'AAU': 1.4016, 'AUU': 1.952, 'CUG': 3.0016, 'CUA': 0.3392, 'CUC': 0.672, 'CAC': 0.8383999999999999, 'AAA': 2.1248, 'CCG': 1.7087999999999999, 'AGU': 0.4608, 'CCA': 0.4224, 'CAA': 0.7744, 'CCC': 0.4096, 'UAU': 1.0752000000000002, 'GGU': 1.3632, 'UGU': 0.37760000000000005, 'CGA': 0.2752, 'CAG': 1.7728, 'UCU': 0.3648, 'GAU': 2.4255999999999998, 'CGG': 0.26239999999999997, 'UUU': 1.2608, 'UGC': 0.512, 'GGG': 0.5504, 'UAG': 1e-06, 'GGA': 0.5888, 'UAA': 0.1152, 'GGC': 2.1376, 'UAC': 0.9344, 'UUC': 0.96, 'UCG': 0.512, 'UUA': 0.9728, 'UUG': 0.7616, 'UCC': 0.352, 'ACC': 1.4592, 'UCA': 0.4992, 'GCA': 1.3504, 'GUA': 0.736, 'GCC': 2.0224, 'GUC': 0.7487999999999999, 'GCG': 2.464, 'GUG': 1.6896, 'GAG': 1.1776, 'GUU': 1.0752000000000002, 'GCU': 0.6848, 'UGA': 0.064, 'GAC': 1.312, 'CGU': 1.3504, 'UGG': 0.6848, 'GAA': 2.7968, 'CGC': 1.664}" | 990 composition="{'CUU': 0.7616, 'AUG': 1.5872, 'ACA': 0.4096, 'ACG': 0.736, 'AUC': 1.1648, 'AAC': 1.5615999999999999, 'AUA': 0.2368, 'AGG': 0.1024, 'CCU': 0.5376000000000001, 'ACU': 0.512, 'AGC': 1.0624, 'AAG': 0.7744, 'AGA': 0.0896, 'CAU': 1.0112, 'AAU': 1.4016, 'AUU': 1.952, 'CUG': 3.0016, 'CUA': 0.3392, 'CUC': 0.672, 'CAC': 0.8383999999999999, 'AAA': 2.1248, 'CCG': 1.7087999999999999, 'AGU': 0.4608, 'CCA': 0.4224, 'CAA': 0.7744, 'CCC': 0.4096, 'UAU': 1.0752000000000002, 'GGU': 1.3632, 'UGU': 0.37760000000000005, 'CGA': 0.2752, 'CAG': 1.7728, 'UCU': 0.3648, 'GAU': 2.4255999999999998, 'CGG': 0.26239999999999997, 'UUU': 1.2608, 'UGC': 0.512, 'GGG': 0.5504, 'UAG': 1e-06, 'GGA': 0.5888, 'UAA': 0.1152, 'GGC': 2.1376, 'UAC': 0.9344, 'UUC': 0.96, 'UCG': 0.512, 'UUA': 0.9728, 'UUG': 0.7616, 'UCC': 0.352, 'ACC': 1.4592, 'UCA': 0.4992, 'GCA': 1.3504, 'GUA': 0.736, 'GCC': 2.0224, 'GUC': 0.7487999999999999, 'GCG': 2.464, 'GUG': 1.6896, 'GAG': 1.1776, 'GUU': 1.0752000000000002, 'GCU': 0.6848, 'UGA': 0.064, 'GAC': 1.312, 'CGU': 1.3504, 'UGG': 0.6848, 'GAA': 2.7968, 'CGC': 1.664}" |
990 elif comp.lower() == 'homosapiens' : | 991 elif comp.lower() == 'homosapiens' : |
995 elif comp.lower() == 'saccharomycescerevisiae' : | 996 elif comp.lower() == 'saccharomycescerevisiae' : |
996 if(altype=="codonsT"): | 997 if(altype=="codonsT"): |
997 composition="{'CTT': 0.7872, 'ATG': 1.3376, 'ACA': 1.1392, 'ACG': 0.512, 'ATC': 1.1008, 'AAC': 1.5872, 'ATA': 1.1392, 'AGG': 0.5888, 'CCT': 0.864, 'ACT': 1.2992000000000001, 'AGC': 0.6272000000000001, 'AAG': 1.9712, 'AGA': 1.3632, 'CAT': 0.8704, 'AAT': 2.2848, 'ATT': 1.9264000000000001, 'CTG': 0.672, 'CTA': 0.8576, 'CTC': 0.3456, 'CAC': 0.4992, 'AAA': 2.6816, 'CCG': 0.3392, 'AGT': 0.9087999999999999, 'CCA': 1.1712, 'CAA': 1.7472, 'CCC': 0.4352, 'TAT': 1.2032, 'GGT': 1.5295999999999998, 'TGT': 0.5184, 'CGA': 0.192, 'CAG': 0.7744, 'TCT': 1.504, 'GAT': 2.4064, 'CGG': 0.1088, 'TTT': 1.6704, 'TGC': 0.3072, 'GGG': 0.384, 'TAG': 0.032, 'GGA': 0.6976, 'TAA': 0.0704, 'GGC': 0.6272000000000001, 'TAC': 0.9472, 'TTC': 1.1776, 'TCG': 0.5504, 'TTA': 1.6767999999999998, 'TTG': 1.7408, 'TCC': 0.9087999999999999, 'ACC': 0.8128, 'TCA': 1.1967999999999999, 'GCA': 1.0368, 'GTA': 0.7552000000000001, 'GCC': 0.8064, 'GTC': 0.7552000000000001, 'GCG': 0.3968, 'GTG': 0.6912, 'GAG': 1.2288, 'GTT': 1.4144, 'GCT': 1.3568, 'TGA': 0.0448, 'GAC': 1.2928, 'CGT': 0.4096, 'TGG': 0.6656, 'GAA': 2.9184, 'CGC': 0.1664}" | 998 composition="{'CTT': 0.7872, 'ATG': 1.3376, 'ACA': 1.1392, 'ACG': 0.512, 'ATC': 1.1008, 'AAC': 1.5872, 'ATA': 1.1392, 'AGG': 0.5888, 'CCT': 0.864, 'ACT': 1.2992000000000001, 'AGC': 0.6272000000000001, 'AAG': 1.9712, 'AGA': 1.3632, 'CAT': 0.8704, 'AAT': 2.2848, 'ATT': 1.9264000000000001, 'CTG': 0.672, 'CTA': 0.8576, 'CTC': 0.3456, 'CAC': 0.4992, 'AAA': 2.6816, 'CCG': 0.3392, 'AGT': 0.9087999999999999, 'CCA': 1.1712, 'CAA': 1.7472, 'CCC': 0.4352, 'TAT': 1.2032, 'GGT': 1.5295999999999998, 'TGT': 0.5184, 'CGA': 0.192, 'CAG': 0.7744, 'TCT': 1.504, 'GAT': 2.4064, 'CGG': 0.1088, 'TTT': 1.6704, 'TGC': 0.3072, 'GGG': 0.384, 'TAG': 0.032, 'GGA': 0.6976, 'TAA': 0.0704, 'GGC': 0.6272000000000001, 'TAC': 0.9472, 'TTC': 1.1776, 'TCG': 0.5504, 'TTA': 1.6767999999999998, 'TTG': 1.7408, 'TCC': 0.9087999999999999, 'ACC': 0.8128, 'TCA': 1.1967999999999999, 'GCA': 1.0368, 'GTA': 0.7552000000000001, 'GCC': 0.8064, 'GTC': 0.7552000000000001, 'GCG': 0.3968, 'GTG': 0.6912, 'GAG': 1.2288, 'GTT': 1.4144, 'GCT': 1.3568, 'TGA': 0.0448, 'GAC': 1.2928, 'CGT': 0.4096, 'TGG': 0.6656, 'GAA': 2.9184, 'CGC': 0.1664}" |
998 else: | 999 else: |
999 composition="{'CUU': 0.7872, 'AUG': 1.3376, 'ACA': 1.1392, 'ACG': 0.512, 'AUC': 1.1008, 'AAC': 1.5872, 'AUA': 1.1392, 'AGG': 0.5888, 'CCU': 0.864, 'ACU': 1.2992000000000001, 'AGC': 0.6272000000000001, 'AAG': 1.9712, 'AGA': 1.3632, 'CAU': 0.8704, 'AAU': 2.2848, 'AUU': 1.9264000000000001, 'CUG': 0.672, 'CUA': 0.8576, 'CUC': 0.3456, 'CAC': 0.4992, 'AAA': 2.6816, 'CCG': 0.3392, 'AGU': 0.9087999999999999, 'CCA': 1.1712, 'CAA': 1.7472, 'CCC': 0.4352, 'UAU': 1.2032, 'GGU': 1.5295999999999998, 'UGU': 0.5184, 'CGA': 0.192, 'CAG': 0.7744, 'UCU': 1.504, 'GAU': 2.4064, 'CGG': 0.1088, 'UUU': 1.6704, 'UGC': 0.3072, 'GGG': 0.384, 'UAG': 0.032, 'GGA': 0.6976, 'UAA': 0.0704, 'GGC': 0.6272000000000001, 'UAC': 0.9472, 'UUC': 1.1776, 'UCG': 0.5504, 'UUA': 1.6767999999999998, 'UUG': 1.7408, 'UCC': 0.9087999999999999, 'ACC': 0.8128, 'UCA': 1.1967999999999999, 'GCA': 1.0368, 'GUA': 0.7552000000000001, 'GCC': 0.8064, 'GUC': 0.7552000000000001, 'GCG': 0.3968, 'GUG': 0.6912, 'GAG': 1.2288, 'GUU': 1.4144, 'GCU': 1.3568, 'UGA': 0.0448, 'GAC': 1.2928, 'CGU': 0.4096, 'UGG': 0.6656, 'GAA': 2.9184, 'CGC': 0.1664}" | 1000 composition="{'CUU': 0.7872, 'AUG': 1.3376, 'ACA': 1.1392, 'ACG': 0.512, 'AUC': 1.1008, 'AAC': 1.5872, 'AUA': 1.1392, 'AGG': 0.5888, 'CCU': 0.864, 'ACU': 1.2992000000000001, 'AGC': 0.6272000000000001, 'AAG': 1.9712, 'AGA': 1.3632, 'CAU': 0.8704, 'AAU': 2.2848, 'AUU': 1.9264000000000001, 'CUG': 0.672, 'CUA': 0.8576, 'CUC': 0.3456, 'CAC': 0.4992, 'AAA': 2.6816, 'CCG': 0.3392, 'AGU': 0.9087999999999999, 'CCA': 1.1712, 'CAA': 1.7472, 'CCC': 0.4352, 'UAU': 1.2032, 'GGU': 1.5295999999999998, 'UGU': 0.5184, 'CGA': 0.192, 'CAG': 0.7744, 'UCU': 1.504, 'GAU': 2.4064, 'CGG': 0.1088, 'UUU': 1.6704, 'UGC': 0.3072, 'GGG': 0.384, 'UAG': 0.032, 'GGA': 0.6976, 'UAA': 0.0704, 'GGC': 0.6272000000000001, 'UAC': 0.9472, 'UUC': 1.1776, 'UCG': 0.5504, 'UUA': 1.6767999999999998, 'UUG': 1.7408, 'UCC': 0.9087999999999999, 'ACC': 0.8128, 'UCA': 1.1967999999999999, 'GCA': 1.0368, 'GUA': 0.7552000000000001, 'GCC': 0.8064, 'GUC': 0.7552000000000001, 'GCG': 0.3968, 'GUG': 0.6912, 'GAG': 1.2288, 'GUU': 1.4144, 'GCU': 1.3568, 'UGA': 0.0448, 'GAC': 1.2928, 'CGU': 0.4096, 'UGG': 0.6656, 'GAA': 2.9184, 'CGC': 0.1664}" |
1000 elif comp.lower() == 'auto' or comp.lower() == 'automatic': | 1001 |
1002 | |
1003 if comp.lower() == 'auto' or comp.lower() == 'automatic': | |
1001 if alphabet == unambiguous_protein_alphabet : | 1004 if alphabet == unambiguous_protein_alphabet : |
1002 prior = weight * asarray(aa_composition, float64) | 1005 prior = weight * asarray(aa_composition, float64) |
1003 else : | 1006 else : |
1004 prior = weight * equiprobable_distribution(len(alphabet)) | 1007 prior = weight * equiprobable_distribution(len(alphabet)) |
1005 elif comp in std_percentCG : | 1008 elif comp in std_percentCG : |
1009 prior = weight * base_distribution( float(comp[:-1])) | 1012 prior = weight * base_distribution( float(comp[:-1])) |
1010 return prior | 1013 return prior |
1011 elif isfloat(comp) : | 1014 elif isfloat(comp) : |
1012 prior = weight * base_distribution( float(comp)*100. ) | 1015 prior = weight * base_distribution( float(comp)*100. ) |
1013 return prior | 1016 return prior |
1014 if composition[0] == '{' and composition[-1] == '}' : | 1017 elif composition[0] == '{' and composition[-1] == '}' : |
1015 explicit = composition[1: -1] | 1018 explicit = composition[1: -1] |
1016 explicit = explicit.replace(',',' ').replace("'", ' ').replace('"',' ').replace(':', ' ').split() | 1019 explicit = explicit.replace(',',' ').replace("'", ' ').replace('"',' ').replace(':', ' ').split() |
1017 | 1020 |
1018 if len(explicit) != len(alphabet)*2 : | 1021 if len(explicit) != len(alphabet)*2 : |
1019 #print explicit | 1022 #print explicit |