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Changeset 10:20716450be87 (2012-01-30)

Previous changeset 9:f3462128e87c (2012-01-30) Next changeset 11:4b38580a8b97 (2012-02-16)

Commit message:
Uploaded

modified:
Codonlogo.xml
codonlogo
weblogolib/__init__.py

added:
test.eps

diff -r f3462128e87c -r 20716450be87 Codonlogo.xml
--- a/Codonlogo.xml Mon Jan 30 08:17:57 2012 -0500
+++ b/Codonlogo.xml Mon Jan 30 21:17:50 2012 -0500

@@ -407,8 +407,8 @@
         <option value="none" >No small sample correction</option>
         <option value="equiprobable" >Equiprobable</option>
         <option value="Homosapiens" >Human</option>
-        <option value="Yeast" >Saccharomycescerevisiae</option>
-        <option value="E.Coli" >Escherichiacoli</option>
+        <option value="Saccharomycescerevisiae" >Yeast</option>
+        <option value="Escherichiacoli" >E.Coli</option>
         <option value="From File">from file</option>

       </param>

diff -r f3462128e87c -r 20716450be87 test.eps
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.eps Mon Jan 30 21:17:50 2012 -0500

[

b"@@ -0,0 +1,1247 @@\n+%!PS-Adobe-3.0 EPSF-3.0\n+%%Title: Sequence Logo: \n+%%Creator: ('CodonLogo 1.1 (2011-09-17)',)\n+%%CreationDate: 2012-01-30 20:49:03.377996\n+%%BoundingBox: 0 0 270 126 \n+%%Pages: 0\n+%%DocumentFonts: \n+%%EndComments\n+\n+\n+% ---- VARIABLES ----\n+\n+/True true def\n+/False false def\n+\n+/debug False def\n+\n+/logo_height 126 def\n+/logo_width 270 def\n+/logo_title () def\n+/show_title False def\n+\n+/logo_margin 2 def\n+/xaxis_label_height 6.0 def\n+/title_height 0 def\n+/stroke_width 0.5 def\n+/tic_length 5 def\n+\n+/lines_per_logo 1 def\n+/line_width 266.8 def\n+/line_height 116.0 def\n+/line_margin_left 30.0 def\n+/line_margin_right 10 def\n+/line_margin_bottom 12.0 def\n+/line_margin_top 4 def\n+\n+/stack_width 32.4 def\n+/stack_height 100 def\n+/stacks_per_line 7 def\n+/stack_margin 0.5 def\n+\n+/show_yaxis True def \n+/show_yaxis_label True def\n+/yaxis_label (bits) def\n+/yaxis_scale 6.0 def % height in units \n+/yaxis_tic_interval 1.0 def % in units\n+/yaxis_minor_tic_interval 0.2 def % in units\n+\n+/show_xaxis_label False def % True or False\n+/show_xaxis True def % True or False\n+/xaxis_label () def\n+/xaxis_tic_interval 1 def\n+/rotate_numbers False def % True or False\n+/number_interval 5 def\n+/show_ends False def \n+/end_type (-) def % d: DNA, p: PROTEIN, -: none\n+\n+/show_fineprint True def\n+/fineprint (CodonLogo 1.1) def\n+/logo_label () def\n+\n+/show_boxes False def % True or False\n+/shrink false def % True or False\n+/shrink_fraction 0.5 def \n+\n+/show_errorbars True def % True or False\n+/errorbar_fraction 0.9 def\n+/errorbar_width_fraction 0.25 def\n+/errorbar_gray 0.5 def\n+\n+/fontsize 10 def\n+/small_fontsize 6 def\n+/title_fontsize 12 def\n+/number_fontsize 8 def\n+\n+\n+/UseCIEColor true def % Fix for issue 4\n+/default_color [ 0.0 0.0 0.0 ] def \n+/color_dict << \n+ (CAT) [ 0.0 1.0 1.0 ]\n+ (CAU) [ 0.0 1.0 1.0 ]\n+ (CAC) [ 0.0 1.0 1.0 ]\n+ (AAA) [ 0.0 1.0 1.0 ]\n+ (AAG) [ 0.0 1.0 1.0 ]\n+ (CGT) [ 0.0 1.0 1.0 ]\n+ (CGU) [ 0.0 1.0 1.0 ]\n+ (CGC) [ 0.0 1.0 1.0 ]\n+ (CGA) [ 0.0 1.0 1.0 ]\n+ (CGG) [ 0.0 1.0 1.0 ]\n+ (AGA) [ 0.0 1.0 1.0 ]\n+ (AGG) [ 0.0 1.0 1.0 ]\n+ (GAT) [ 1.0 0.0 0.0 ]\n+ (GAU) [ 1.0 0.0 0.0 ]\n+ (GAC) [ 1.0 0.0 0.0 ]\n+ (GAA) [ 1.0 0.0 0.0 ]\n+ (GAG) [ 1.0 0.0 0.0 ]\n+ (TCT) [ 0.0 1.0 0.0 ]\n+ (UCU) [ 0.0 1.0 0.0 ]\n+ (TCC) [ 0.0 1.0 0.0 ]\n+ (UCC) [ 0.0 1.0 0.0 ]\n+ (TCA) [ 0.0 1.0 0.0 ]\n+ (UCA) [ 0.0 1.0 0.0 ]\n+ (TCG) [ 0.0 1.0 0.0 ]\n+ (UCG) [ 0.0 1.0 0.0 ]\n+ (AGT) [ 0.0 1.0 0.0 ]\n+ (AGU) [ 0.0 1.0 0.0 ]\n+ (AGC) [ 0.0 1.0 0.0 ]\n+ (ACT) [ 0.0 1.0 0.0 ]\n+ (ACU) [ 0.0 1.0 0.0 ]\n+ (ACC) [ 0.0 1.0 0.0 ]\n+ (ACA) [ 0.0 1.0 0.0 ]\n+ (ACG) [ 0.0 1.0 0.0 ]\n+ (CAA) [ 0.0 1.0 0.0 ]\n+ (CAG) [ 0.0 1.0 0.0 ]\n+ (AAT) [ 0.0 1.0 0.0 ]\n+ (AAU) [ 0.0 1.0 0.0 ]\n+ (AAC) [ 0.0 1.0 0.0 ]\n+ (GCT) [ 0.333333333333 0.333333333333 1.0 ]\n+ (GCU) [ 0.333333333333 0.333333333333 1.0 ]\n+ (GCC) [ 0.333333333333 0.333333333333 1.0 ]\n+ (GCA) [ 0.333333333333 0.333333333333 1.0 ]\n+ (GCG) [ 0.333333333333 0.333333333333 1.0 ]\n+ (GTT) [ 0.333333333333 0.333333333333 1.0 ]\n+ (GUU) [ 0.333333333333 0.333333333333 1.0 ]\n+ (GTC) [ 0.333333333333 0.333333333333 1.0 ]\n+ (GUC) [ 0.333333333333 0.333333333333 1.0 ]\n+ (GTA) [ 0.333333333333 0.333333333333 1.0 ]\n+ (GUA) [ 0.333333333333 0.333333333333 1.0 ]\n+ (GTG) [ 0.333333333333 0.333333333333 1.0 ]\n+ (GUG) [ 0.333333333333 0.333333333333 1.0 ]\n+ (CTT) [ 0.333333333333 0.333333333333 1.0 ]\n+ (CUU) [ 0.333333333333 0.333333333333 1.0 ]\n+ (CTC) [ 0.333333333333 0.333333333333 1.0 ]\n+ ("..b' ShowSymbol\n+ 1.000000 0.000000 (GCA) ShowSymbol\n+ 1.000000 0.000000 (GAT) ShowSymbol\n+ 1.000000 0.000000 (GAG) ShowSymbol\n+ 1.000000 0.000000 (GAC) ShowSymbol\n+ 1.000000 0.000000 (GAA) ShowSymbol\n+ 1.000000 0.000000 (CTT) ShowSymbol\n+ 1.000000 0.000000 (CTG) ShowSymbol\n+ 1.000000 0.000000 (CGG) ShowSymbol\n+ 1.000000 0.000000 (CCT) ShowSymbol\n+ 1.000000 0.000000 (CCG) ShowSymbol\n+ 1.000000 0.000000 (CCC) ShowSymbol\n+ 1.000000 0.000000 (CCA) ShowSymbol\n+ 1.000000 0.000000 (CAG) ShowSymbol\n+ 1.000000 0.000000 (ATG) ShowSymbol\n+ 1.000000 0.000000 (ATC) ShowSymbol\n+ 1.000000 0.000000 (ATA) ShowSymbol\n+ 1.000000 0.000000 (AGT) ShowSymbol\n+ 1.000000 0.000000 (AGG) ShowSymbol\n+ 1.000000 0.000000 (AGC) ShowSymbol\n+ 1.000000 0.000000 (AGA) ShowSymbol\n+ 1.000000 0.000000 (ACT) ShowSymbol\n+ 1.000000 0.000000 (ACG) ShowSymbol\n+ 1.000000 0.000000 (ACC) ShowSymbol\n+ 1.000000 0.000000 (AAT) ShowSymbol\n+ 1.000000 0.000000 (AAG) ShowSymbol\n+ 1.000000 0.021747 (TGC) ShowSymbol\n+ 1.000000 0.021747 (TAC) ShowSymbol\n+ 1.000000 0.021747 (TAA) ShowSymbol\n+ 1.000000 0.021747 (CTC) ShowSymbol\n+ 1.000000 0.021747 (CTA) ShowSymbol\n+ 1.000000 0.021747 (ATT) ShowSymbol\n+ 1.000000 0.021747 (ACA) ShowSymbol\n+ 1.000000 0.021747 (AAA) ShowSymbol\n+ 1.000000 0.043493 (CGA) ShowSymbol\n+ 1.000000 0.065240 (CGT) ShowSymbol\n+ 1.000000 0.065240 (CAT) ShowSymbol\n+ 1.000000 0.086986 (CGC) ShowSymbol\n+ 1.000000 0.086986 (CAA) ShowSymbol\n+ 1.000000 0.086986 (AAC) ShowSymbol\n+ 1.000000 0.456677 (CAC) ShowSymbol\n+ 0.320681 0.320681 DrawErrorbar\n+EndStack\n+\n+(7) StartStack\n+ 1.000000 0.000000 (TTG) ShowSymbol\n+ 1.000000 0.000000 (TTA) ShowSymbol\n+ 1.000000 0.000000 (TGG) ShowSymbol\n+ 1.000000 0.000000 (TGC) ShowSymbol\n+ 1.000000 0.000000 (TGA) ShowSymbol\n+ 1.000000 0.000000 (TCG) ShowSymbol\n+ 1.000000 0.000000 (TCC) ShowSymbol\n+ 1.000000 0.000000 (TAT) ShowSymbol\n+ 1.000000 0.000000 (TAG) ShowSymbol\n+ 1.000000 0.000000 (TAC) ShowSymbol\n+ 1.000000 0.000000 (TAA) ShowSymbol\n+ 1.000000 0.000000 (GTG) ShowSymbol\n+ 1.000000 0.000000 (GTC) ShowSymbol\n+ 1.000000 0.000000 (GTA) ShowSymbol\n+ 1.000000 0.000000 (GGT) ShowSymbol\n+ 1.000000 0.000000 (GGG) ShowSymbol\n+ 1.000000 0.000000 (GGC) ShowSymbol\n+ 1.000000 0.000000 (GCG) ShowSymbol\n+ 1.000000 0.000000 (GCC) ShowSymbol\n+ 1.000000 0.000000 (GCA) ShowSymbol\n+ 1.000000 0.000000 (GAT) ShowSymbol\n+ 1.000000 0.000000 (GAG) ShowSymbol\n+ 1.000000 0.000000 (GAC) ShowSymbol\n+ 1.000000 0.000000 (CTT) ShowSymbol\n+ 1.000000 0.000000 (CTG) ShowSymbol\n+ 1.000000 0.000000 (CTC) ShowSymbol\n+ 1.000000 0.000000 (CTA) ShowSymbol\n+ 1.000000 0.000000 (CGT) ShowSymbol\n+ 1.000000 0.000000 (CGG) ShowSymbol\n+ 1.000000 0.000000 (CGC) ShowSymbol\n+ 1.000000 0.000000 (CGA) ShowSymbol\n+ 1.000000 0.000000 (CCT) ShowSymbol\n+ 1.000000 0.000000 (CCG) ShowSymbol\n+ 1.000000 0.000000 (CCC) ShowSymbol\n+ 1.000000 0.000000 (CCA) ShowSymbol\n+ 1.000000 0.000000 (CAG) ShowSymbol\n+ 1.000000 0.000000 (CAC) ShowSymbol\n+ 1.000000 0.000000 (ATG) ShowSymbol\n+ 1.000000 0.000000 (ATC) ShowSymbol\n+ 1.000000 0.000000 (AGG) ShowSymbol\n+ 1.000000 0.000000 (AGC) ShowSymbol\n+ 1.000000 0.000000 (ACG) ShowSymbol\n+ 1.000000 0.000000 (ACC) ShowSymbol\n+ 1.000000 0.000000 (AAG) ShowSymbol\n+ 1.000000 0.000000 (AAC) ShowSymbol\n+ 1.000000 0.017469 (TTC) ShowSymbol\n+ 1.000000 0.017469 (TGT) ShowSymbol\n+ 1.000000 0.017469 (TCT) ShowSymbol\n+ 1.000000 0.017469 (TCA) ShowSymbol\n+ 1.000000 0.017469 (GGA) ShowSymbol\n+ 1.000000 0.017469 (GCT) ShowSymbol\n+ 1.000000 0.017469 (GAA) ShowSymbol\n+ 1.000000 0.017469 (ACA) ShowSymbol\n+ 1.000000 0.034937 (TTT) ShowSymbol\n+ 1.000000 0.034937 (CAT) ShowSymbol\n+ 1.000000 0.034937 (CAA) ShowSymbol\n+ 1.000000 0.034937 (AGT) ShowSymbol\n+ 1.000000 0.052406 (GTT) ShowSymbol\n+ 1.000000 0.052406 (AGA) ShowSymbol\n+ 1.000000 0.052406 (AAT) ShowSymbol\n+ 1.000000 0.069875 (AAA) ShowSymbol\n+ 1.000000 0.087344 (ATA) ShowSymbol\n+ 1.000000 0.087344 (ACT) ShowSymbol\n+ 1.000000 0.174687 (ATT) ShowSymbol\n+ 0.295737 0.295737 DrawErrorbar\n+EndStack\n+\n+EndLine\n+\n+EndLogo\n+\n+\n+%%EOF\n+\n'

diff -r f3462128e87c -r 20716450be87 weblogolib/__init__.py
--- a/weblogolib/__init__.py Mon Jan 30 08:17:57 2012 -0500
+++ b/weblogolib/__init__.py Mon Jan 30 21:17:50 2012 -0500

[

b'@@ -983,11 +983,20 @@\n prior = weight * equiprobable_distribution(len(alphabet)) \n \n elif comp.lower() == \'escherichiacoli\' :\n-\tcomposition="{\'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}"\n+ if(altype=="codonsT"):\n+ 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}"\n+ else:\n+ 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}"\n elif comp.lower() == \'homosapiens\' :\n-\tcomposition="{\'CTT\': 0.8448, \'ATG\': 1.408, \'ACA\': 0.9663999999999999, \'ACG\': 0.39039999999999997, \'ATC\': 1.3312, \'AAC\': 1.2224000000000002, \'ATA\': 0.48, \'AGG\': 0.768, \'CCT\': 1.12, \'ACT\': 0.8383999999999999, \'AGC\': 1.248, \'AAG\': 2.0416, \'AGA\': 0.7807999999999999, \'CAT\': 0.6976, \'AAT\': 1.088, \'ATT\': 1.024, \'CTG\': 2.5344, \'CTA\': 0.4608, \'CTC\': 1.2544000000000002, \'CAC\': 0.9663999999999999, \'AAA\': 1.5615999999999999, \'CCG\': 0.44160000000000005, \'AGT\': 0.7744, \'CCA\': 1.0816, \'CAA\': 0.7872, \'CCC\': 1.2'..b' \'AUG\': 1.408, \'ACA\': 0.9663999999999999, \'ACG\': 0.39039999999999997, \'AUC\': 1.3312, \'AAC\': 1.2224000000000002, \'AUA\': 0.48, \'AGG\': 0.768, \'CCU\': 1.12, \'ACU\': 0.8383999999999999, \'AGC\': 1.248, \'AAG\': 2.0416, \'AGA\': 0.7807999999999999, \'CAU\': 0.6976, \'AAU\': 1.088, \'AUU\': 1.024, \'CUG\': 2.5344, \'CUA\': 0.4608, \'CUC\': 1.2544000000000002, \'CAC\': 0.9663999999999999, \'AAA\': 1.5615999999999999, \'CCG\': 0.44160000000000005, \'AGU\': 0.7744, \'CCA\': 1.0816, \'CAA\': 0.7872, \'CCC\': 1.2672, \'UAU\': 0.7807999999999999, \'GGU\': 0.6912, \'UGU\': 0.6784, \'CGA\': 0.3968, \'CAG\': 2.1888, \'UCU\': 0.9728, \'GAU\': 1.3952, \'CGG\': 0.7296, \'UUU\': 1.1264, \'UGC\': 0.8064, \'GGG\': 1.056, \'UAG\': 0.0512, \'GGA\': 1.056, \'UAA\': 0.064, \'GGC\': 1.4208, \'UAC\': 0.9792000000000001, \'UUC\': 1.2992000000000001, \'UCG\': 0.2816, \'UUA\': 0.4928, \'UUG\': 0.8256, \'UCC\': 1.1328, \'ACC\': 1.2096, \'UCA\': 0.7807999999999999, \'GCA\': 1.0112, \'GUA\': 0.45439999999999997, \'GCC\': 1.7728, \'GUC\': 0.928, \'GCG\': 0.4736, \'GUG\': 1.7984, \'GAG\': 2.5344, \'GUU\': 0.704, \'GCU\': 1.1776, \'UGA\': 0.1024, \'GAC\': 1.6064, \'CGU\': 0.288, \'UGG\': 0.8448, \'GAA\': 1.856, \'CGC\': 0.6656}"\n+ elif comp.lower() == \'saccharomycescerevisiae\' : \n+ if(altype=="codonsT"):\n+ 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}"\n+ else:\n+ 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}"\n elif comp.lower() == \'auto\' or comp.lower() == \'automatic\':\n if alphabet == unambiguous_protein_alphabet :\n prior = weight * asarray(aa_composition, float64)\n@@ -1002,7 +1011,7 @@\n elif isfloat(comp) :\n prior = weight * base_distribution( float(comp)*100. )\n \n- elif composition[0] == \'{\' and composition[-1] == \'}\' : \n+ if composition[0] == \'{\' and composition[-1] == \'}\' : \n explicit = composition[1: -1]\n explicit = explicit.replace(\',\',\' \').replace("\'", \' \').replace(\'"\',\' \').replace(\':\', \' \').split()\n \n'