Mercurial > repos > davidmurphy > codonlogo
changeset 10:20716450be87
Uploaded
| author | davidmurphy |
|---|---|
| date | Mon, 30 Jan 2012 21:17:50 -0500 |
| parents | f3462128e87c |
| children | 4b38580a8b97 |
| files | Codonlogo.xml codonlogo test.eps weblogolib/__init__.py |
| diffstat | 3 files changed, 1263 insertions(+), 7 deletions(-) [+] |
line wrap: on
line diff
--- 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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test.eps Mon Jan 30 21:17:50 2012 -0500 @@ -0,0 +1,1247 @@ +%!PS-Adobe-3.0 EPSF-3.0 +%%Title: Sequence Logo: +%%Creator: ('CodonLogo 1.1 (2011-09-17)',) +%%CreationDate: 2012-01-30 20:49:03.377996 +%%BoundingBox: 0 0 270 126 +%%Pages: 0 +%%DocumentFonts: +%%EndComments + + +% ---- VARIABLES ---- + +/True true def +/False false def + +/debug False def + +/logo_height 126 def +/logo_width 270 def +/logo_title () def +/show_title False def + +/logo_margin 2 def +/xaxis_label_height 6.0 def +/title_height 0 def +/stroke_width 0.5 def +/tic_length 5 def + +/lines_per_logo 1 def +/line_width 266.8 def +/line_height 116.0 def +/line_margin_left 30.0 def +/line_margin_right 10 def +/line_margin_bottom 12.0 def +/line_margin_top 4 def + +/stack_width 32.4 def +/stack_height 100 def +/stacks_per_line 7 def +/stack_margin 0.5 def + +/show_yaxis True def +/show_yaxis_label True def +/yaxis_label (bits) def +/yaxis_scale 6.0 def % height in units +/yaxis_tic_interval 1.0 def % in units +/yaxis_minor_tic_interval 0.2 def % in units + +/show_xaxis_label False def % True or False +/show_xaxis True def % True or False +/xaxis_label () def +/xaxis_tic_interval 1 def +/rotate_numbers False def % True or False +/number_interval 5 def +/show_ends False def +/end_type (-) def % d: DNA, p: PROTEIN, -: none + +/show_fineprint True def +/fineprint (CodonLogo 1.1) def +/logo_label () def + +/show_boxes False def % True or False +/shrink false def % True or False +/shrink_fraction 0.5 def + +/show_errorbars True def % True or False +/errorbar_fraction 0.9 def +/errorbar_width_fraction 0.25 def +/errorbar_gray 0.5 def + +/fontsize 10 def +/small_fontsize 6 def +/title_fontsize 12 def +/number_fontsize 8 def + + +/UseCIEColor true def % Fix for issue 4 +/default_color [ 0.0 0.0 0.0 ] def +/color_dict << + (CAT) [ 0.0 1.0 1.0 ] + (CAU) [ 0.0 1.0 1.0 ] + (CAC) [ 0.0 1.0 1.0 ] + (AAA) [ 0.0 1.0 1.0 ] + (AAG) [ 0.0 1.0 1.0 ] + (CGT) [ 0.0 1.0 1.0 ] + (CGU) [ 0.0 1.0 1.0 ] + (CGC) [ 0.0 1.0 1.0 ] + (CGA) [ 0.0 1.0 1.0 ] + (CGG) [ 0.0 1.0 1.0 ] + (AGA) [ 0.0 1.0 1.0 ] + (AGG) [ 0.0 1.0 1.0 ] + (GAT) [ 1.0 0.0 0.0 ] + (GAU) [ 1.0 0.0 0.0 ] + (GAC) [ 1.0 0.0 0.0 ] + (GAA) [ 1.0 0.0 0.0 ] + (GAG) [ 1.0 0.0 0.0 ] + (TCT) [ 0.0 1.0 0.0 ] + (UCU) [ 0.0 1.0 0.0 ] + (TCC) [ 0.0 1.0 0.0 ] + (UCC) [ 0.0 1.0 0.0 ] + (TCA) [ 0.0 1.0 0.0 ] + (UCA) [ 0.0 1.0 0.0 ] + (TCG) [ 0.0 1.0 0.0 ] + (UCG) [ 0.0 1.0 0.0 ] + (AGT) [ 0.0 1.0 0.0 ] + (AGU) [ 0.0 1.0 0.0 ] + (AGC) [ 0.0 1.0 0.0 ] + (ACT) [ 0.0 1.0 0.0 ] + (ACU) [ 0.0 1.0 0.0 ] + (ACC) [ 0.0 1.0 0.0 ] + (ACA) [ 0.0 1.0 0.0 ] + (ACG) [ 0.0 1.0 0.0 ] + (CAA) [ 0.0 1.0 0.0 ] + (CAG) [ 0.0 1.0 0.0 ] + (AAT) [ 0.0 1.0 0.0 ] + (AAU) [ 0.0 1.0 0.0 ] + (AAC) [ 0.0 1.0 0.0 ] + (GCT) [ 0.333333333333 0.333333333333 1.0 ] + (GCU) [ 0.333333333333 0.333333333333 1.0 ] + (GCC) [ 0.333333333333 0.333333333333 1.0 ] + (GCA) [ 0.333333333333 0.333333333333 1.0 ] + (GCG) [ 0.333333333333 0.333333333333 1.0 ] + (GTT) [ 0.333333333333 0.333333333333 1.0 ] + (GUU) [ 0.333333333333 0.333333333333 1.0 ] + (GTC) [ 0.333333333333 0.333333333333 1.0 ] + (GUC) [ 0.333333333333 0.333333333333 1.0 ] + (GTA) [ 0.333333333333 0.333333333333 1.0 ] + (GUA) [ 0.333333333333 0.333333333333 1.0 ] + (GTG) [ 0.333333333333 0.333333333333 1.0 ] + (GUG) [ 0.333333333333 0.333333333333 1.0 ] + (CTT) [ 0.333333333333 0.333333333333 1.0 ] + (CUU) [ 0.333333333333 0.333333333333 1.0 ] + (CTC) [ 0.333333333333 0.333333333333 1.0 ] + (CUC) [ 0.333333333333 0.333333333333 1.0 ] + (CTA) [ 0.333333333333 0.333333333333 1.0 ] + (CUA) [ 0.333333333333 0.333333333333 1.0 ] + (CTG) [ 0.333333333333 0.333333333333 1.0 ] + (CUG) [ 0.333333333333 0.333333333333 1.0 ] + (TTA) [ 0.333333333333 0.333333333333 1.0 ] + (UUA) [ 0.333333333333 0.333333333333 1.0 ] + (TTG) [ 0.333333333333 0.333333333333 1.0 ] + (UUG) [ 0.333333333333 0.333333333333 1.0 ] + (ATT) [ 0.333333333333 0.333333333333 1.0 ] + (AUU) [ 0.333333333333 0.333333333333 1.0 ] + (ATC) [ 0.333333333333 0.333333333333 1.0 ] + (AUC) [ 0.333333333333 0.333333333333 1.0 ] + (ATA) [ 0.333333333333 0.333333333333 1.0 ] + (AUA) [ 0.333333333333 0.333333333333 1.0 ] + (ATG) [ 0.333333333333 0.333333333333 1.0 ] + (AUG) [ 0.333333333333 0.333333333333 1.0 ] + (TTT) [ 1.0 0.0 1.0 ] + (UUU) [ 1.0 0.0 1.0 ] + (TTC) [ 1.0 0.0 1.0 ] + (UUC) [ 1.0 0.0 1.0 ] + (TAT) [ 1.0 0.0 1.0 ] + (UAU) [ 1.0 0.0 1.0 ] + (TAC) [ 1.0 0.0 1.0 ] + (UAC) [ 1.0 0.0 1.0 ] + (TGG) [ 1.0 0.0 1.0 ] + (UGG) [ 1.0 0.0 1.0 ] + (GGT) [ 0.6 0.4 0.0 ] + (GGU) [ 0.6 0.4 0.0 ] + (GGC) [ 0.6 0.4 0.0 ] + (GGA) [ 0.6 0.4 0.0 ] + (GGG) [ 0.6 0.4 0.0 ] + (CCT) [ 0.6 0.4 0.0 ] + (CCU) [ 0.6 0.4 0.0 ] + (CCC) [ 0.6 0.4 0.0 ] + (CCA) [ 0.6 0.4 0.0 ] + (CCG) [ 0.6 0.4 0.0 ] + (TGT) [ 1.0 1.0 0.0 ] + (UGU) [ 1.0 1.0 0.0 ] + (TGC) [ 1.0 1.0 0.0 ] + (UGC) [ 1.0 1.0 0.0 ] + (TAA) [ 0.0 0.0 0.0 ] + (UAA) [ 0.0 0.0 0.0 ] + (TAG) [ 0.0 0.0 0.0 ] + (UAG) [ 0.0 0.0 0.0 ] + (TGA) [ 0.0 0.0 0.0 ] + (UGA) [ 0.0 0.0 0.0 ] +>> def + + + +% ---- DERIVED PARAMETERS ---- + +/char_width stack_width 2 stack_margin mul sub def +/char_width2 char_width 2 div def +/char_width4 char_width 4 div def + +% movements to place 5'/N and 3'/C symbols +/leftEndDeltaX fontsize neg def +/leftEndDeltaY fontsize 1.25 mul neg def +/rightEndDeltaX fontsize 0.25 mul def +/rightEndDeltaY leftEndDeltaY def + + +% ---- PROCEDURES ---- + + +/SetTitleFont {/ArialMT findfont title_fontsize scalefont setfont} bind def +/SetLogoFont {/Arial-BoldMT findfont char_width scalefont setfont} bind def +/SetStringFont{/ArialMT findfont fontsize scalefont setfont} bind def +/SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def +/SetSmallFont {/ArialMT findfont small_fontsize scalefont setfont} bind def +/SetNumberFont {/ArialMT findfont number_fontsize scalefont setfont} bind def + +/DrawBox { % width height + /hh exch def + /ww exch def + gsave + 0.2 setlinewidth + %0.5 setgray + + %0 0 moveto + hh 0 rlineto + 0 ww rlineto + hh neg 0 rlineto + 0 ww neg rlineto + stroke + grestore +} bind def + + +/StartLogo { + %save + gsave + + + debug { + logo_margin logo_margin moveto + logo_height logo_margin 2 mul sub + logo_width logo_margin 2 mul sub + DrawBox } if + + show_title { DrawTitle } if + show_xaxis_label { DrawXaxisLable } if + show_fineprint { DrawFineprint } if + DrawLogoLabel + + + MoveToFirstLine +} bind def + + +/DrawLogoLabel { + gsave + SetTitleFont + + logo_margin + logo_height title_fontsize sub logo_margin sub + moveto + + debug { title_fontsize logo_label stringwidth pop DrawBox } if + 0 title_fontsize 4 div rmoveto % Move up to baseline (approximatly) + logo_label show + + grestore +} bind def + +/DrawTitle { + gsave + SetTitleFont + + logo_width 2 div logo_title stringwidth pop 2 div sub + logo_height title_fontsize sub logo_margin sub + moveto + + debug { title_fontsize logo_title stringwidth pop DrawBox } if + + 0 title_fontsize 4 div rmoveto % Move up to baseline (approximatly) + logo_title show + + grestore +} bind def + +/DrawXaxisLable { + % Print X-axis label, bottom center + gsave + SetStringFont + + logo_width 2 div xaxis_label stringwidth pop 2 div sub + xaxis_label_height logo_margin add fontsize sub + moveto + %fontsize 3 div + + debug { fontsize xaxis_label stringwidth pop DrawBox } if + + xaxis_label show + + grestore +} bind def + + +/DrawFineprint { + gsave + + SetSmallFont + + logo_width fineprint stringwidth pop sub + logo_margin sub line_margin_right sub + logo_margin + moveto + + debug { small_fontsize fineprint stringwidth pop DrawBox } if + + fineprint show + grestore +} bind def + +/MoveToFirstLine { + logo_margin + logo_height logo_margin sub title_height sub line_height sub + moveto +} bind def + +/EndLogo { + grestore + %showpage + %restore +} bind def + + +/StartLine{ + gsave + + % Draw outer box + debug { line_height line_width DrawBox } if + + % Move to lower left corner of content area + line_margin_left line_margin_bottom rmoveto + + % Draw inner content box + debug { + line_height line_margin_bottom sub line_margin_top sub + line_width line_margin_left sub line_margin_right sub + DrawBox + } if + + show_yaxis { DrawYaxis } if + show_xaxis { DrawLeftEnd } if + +} bind def + +/EndLine{ + show_xaxis { DrawRightEnd } if + grestore + 0 line_height neg rmoveto +} bind def + + +/DrawYaxis { + gsave + stack_margin neg 0 translate + DrawYaxisBar + DrawYaxisLabel + grestore +} bind def + + +/DrawYaxisBar { + gsave + stack_margin neg 0 rmoveto + + SetNumberFont + stroke_width setlinewidth + + /str 10 string def % string to hold number + /smallgap stack_margin def + + % Draw first tic and bar + gsave + tic_length neg 0 rmoveto + tic_length 0 rlineto + 0 stack_height rlineto + stroke + grestore + + % Draw the tics + % initial increment limit proc for + 0 yaxis_tic_interval yaxis_scale abs + {/loopnumber exch def + + % convert the number coming from the loop to a string + % and find its width + loopnumber 10 str cvrs + /stringnumber exch def % string representing the number + + stringnumber stringwidth pop + /numberwidth exch def % width of number to show + + /halfnumberheight + stringnumber CharBoxHeight 2 div + def + + gsave + numberwidth % move back width of number + neg loopnumber stack_height yaxis_scale div mul % shift on y axis + halfnumberheight sub % down half the digit + rmoveto % move back the width of the string + + tic_length neg smallgap sub % Move back a bit more + 0 rmoveto % move back the width of the tic + + stringnumber show + smallgap 0 rmoveto % Make a small gap + + % now show the tic mark + 0 halfnumberheight rmoveto % shift up again + tic_length 0 rlineto + stroke + grestore + } for + + % Draw the minor tics + % initial increment limit proc for + 0 yaxis_minor_tic_interval yaxis_scale abs + {/loopnumber2 exch def + gsave + 0 + loopnumber2 stack_height yaxis_scale div mul + rmoveto + + tic_length 2 div neg 0 rlineto + stroke + grestore + } for + + grestore +} bind def + +/DrawYaxisLabel { + gsave + SetStringFont + + % How far we move left depends on the size of + % the tic labels. + /str 10 string def % string to hold number + yaxis_scale yaxis_tic_interval div cvi yaxis_tic_interval mul + str cvs stringwidth pop + tic_length 1.25 mul add neg + + stack_height + yaxis_label stringwidth pop + sub 2 div + + rmoveto + 90 rotate + + yaxis_label show + grestore +} bind def + + +%Take a single character and return the bounding box +/CharBox { % <char> CharBox <lx> <ly> <ux> <uy> + gsave + newpath + 0 0 moveto + % take the character off the stack and use it here: + true charpath + flattenpath + pathbbox % compute bounding box of 1 pt. char => lx ly ux uy + % the path is here, but toss it away ... + grestore +} bind def + + +% The height of a characters bounding box +/CharBoxHeight { % <char> CharBoxHeight <num> + CharBox + exch pop sub neg exch pop +} bind def + + +% The width of a characters bounding box +/CharBoxWidth { % <char> CharBoxHeight <num> + CharBox + pop exch pop sub neg +} bind def + + +/DrawLeftEnd { + gsave + SetStringFont + leftEndDeltaX leftEndDeltaY rmoveto + + show_ends { + debug { leftEndDeltaY neg leftEndDeltaX neg DrawBox } if + end_type (d) eq {(5) show DrawPrime} if + end_type (p) eq {(N) show} if + } if + grestore +} bind def + +/DrawRightEnd { + gsave + SetStringFont + rightEndDeltaX rightEndDeltaY rmoveto + + show_ends { + debug { rightEndDeltaY neg leftEndDeltaX neg DrawBox } if + end_type (d) eq {(3) show DrawPrime} if + end_type (p) eq {(C) show} if + } if + grestore +} bind def + +/DrawPrime { + gsave + SetPrimeFont + (\242) show + grestore +} bind def + + +/StartStack { % <stackNumber> startstack + show_xaxis {DrawNumber}{pop} ifelse + gsave + debug { stack_height stack_width DrawBox } if + +} bind def + +/EndStack { + grestore + stack_width 0 rmoveto +} bind def + + +/DrawNumber { % number MakeNumber + /n exch def + + + gsave + %0 stack_margin neg rmoveto + stroke_width setlinewidth + stack_width 0 rlineto + stack_width 2 div neg 0 rmoveto + + n () eq + { 0 tic_length 4 div neg rlineto } + { 0 tic_length 2 div neg rlineto } + ifelse + + stroke + grestore + + + + gsave + n + SetNumberFont + stack_width 2 div tic_length 2 div neg rmoveto + + rotate_numbers { + 90 rotate + dup stringwidth pop neg % find the length of the number + stack_margin sub % Move down a bit + (0) CharBoxHeight 2 div neg % left half height of numbers + rmoveto + show + } { + dup stringwidth pop neg 2 div number_fontsize neg rmoveto + show + } ifelse + + + + grestore +} bind def + + + +% Draw a character whose height is proportional to symbol bits +/ShowSymbol{ % interval character ShowSymbol + /char exch def + /interval exch def + /fraction_width exch def + + /char_height + interval yaxis_scale div stack_height mul + stack_margin sub + dup + % if char_height is negative or very small replace with zero + % BUG FIX: This used to be '0.0 gt' but it seems that DrawHeight + % has a finite, non-zero minimum, which results in a rangecheck error + 0.01 gt {}{pop 0.0} ifelse + def + + char_height 0.0 gt { + show_boxes { + gsave + /ww char_height stack_margin add def + /hh stack_width def + stroke_width setlinewidth + hh 0 rlineto + 0 ww rlineto + hh neg 0 rlineto + 0 ww neg rlineto + stroke + grestore + } if + + gsave + stack_margin stack_margin rmoveto + debug { char_height char_width DrawBox } if + 1 fraction_width sub char_width mul 2 div 0 rmoveto + fraction_width char_width mul char_height char DrawChar + grestore + + } if + 0 interval yaxis_scale div stack_height mul rmoveto +} bind def + + +/DrawChar { % <width> <height> <char> ShowChar + /tc exch def % The character + /ysize exch def % the y size of the character + /xsize exch def % the x size of the character + /xmulfactor 1 def + /ymulfactor 1 def + + gsave + SetLogoFont + tc SetColor + + % IReplacementHack + % Deal with the lack of bars on the letter 'I' in Arial and Helvetica + % by replacing with 'I' from Courier. + tc (I) eq { + /Courier findfont char_width scalefont setfont + } if + + + shrink { + xsize 1 shrink_fraction sub 2 div mul + ysize 1 shrink_fraction sub 2 div mul rmoveto + shrink_fraction shrink_fraction scale + } if + + % Calculate the font scaling factors + % Loop twice to catch small correction due to first scaling + 2 { + gsave + xmulfactor ymulfactor scale + + ysize % desired size of character in points + tc CharBoxHeight + dup 0.0 ne { + div % factor by which to scale up the character + /ymulfactor exch def + } {pop pop} ifelse + + xsize % desired size of character in points + tc CharBoxWidth + dup 0.0 ne { + div % factor by which to scale up the character + /xmulfactor exch def + } {pop pop} ifelse + grestore + } repeat + + + + % Draw the character + xmulfactor ymulfactor scale + % Move lower left corner of character to start point + tc CharBox pop pop % llx lly : Lower left corner + exch neg exch neg + rmoveto + + tc show + + grestore +} bind def + +/SetColor{ % <char> SetColor + dup color_dict exch known { + color_dict exch get aload pop setrgbcolor + } { + pop + default_color aload pop setrgbcolor + } ifelse +} bind def + + +/DrawErrorbar{ % interval_down interval_up DrawErrorbar + + gsave + /points_per_unit stack_height yaxis_scale div def + /height_up exch points_per_unit mul def + /height_down exch points_per_unit mul def + + show_errorbars { + + stroke_width setlinewidth + errorbar_gray setgray + stack_width 2 div 0 rmoveto + + /errorbar_width char_width errorbar_width_fraction mul def + /errorbar_width2 errorbar_width 2 div def + + gsave + 0 height_down neg rmoveto + errorbar_width2 neg 0 rlineto + errorbar_width 0 rlineto + errorbar_width2 neg 0 rlineto + 0 height_down errorbar_fraction mul rlineto + stroke + grestore + + gsave + 0 height_up rmoveto + errorbar_width2 neg 0 rlineto + errorbar_width 0 rlineto + errorbar_width2 neg 0 rlineto + 0 height_up neg errorbar_fraction mul rlineto + stroke + grestore + } if + + grestore + +} bind def + +/DrawErrorbarFirst{ % interval_down interval_up center DrawErrorbarFirst + gsave + /points_per_unit stack_height yaxis_scale div def + /center exch points_per_unit mul def + + 0 center rmoveto + DrawErrorbar + grestore +} bind def + +%%EndProlog + +%%Page: 1 1 + +% Example Data +%StartLogo +% StartLine +% (1) StartStack +% 1.2 (C) ShowSymbol +% 2.2 (I) ShowSymbol +% 0.5 0.5 DrawErrorbar +% EndStack +% (2) StartStack +% 0.5 (I) ShowSymbol +% 0.9 (L) ShowSymbol +% 1.0 (G) ShowSymbol +% +% 0.5 0.5 DrawErrorbar +% EndStack +% (234) StartStack +% EndStack +% (235) StartStack +% EndStack +% EndLine +%EndLogo + +StartLogo + +StartLine +(1) StartStack + 1.000000 0.000000 (TTC) ShowSymbol + 1.000000 0.000000 (TGT) ShowSymbol + 1.000000 0.000000 (TGG) ShowSymbol + 1.000000 0.000000 (TGA) ShowSymbol + 1.000000 0.000000 (TCG) ShowSymbol + 1.000000 0.000000 (TCC) ShowSymbol + 1.000000 0.000000 (TCA) ShowSymbol + 1.000000 0.000000 (TAT) ShowSymbol + 1.000000 0.000000 (TAG) ShowSymbol + 1.000000 0.000000 (TAC) ShowSymbol + 1.000000 0.000000 (GTT) ShowSymbol + 1.000000 0.000000 (GTC) ShowSymbol + 1.000000 0.000000 (GTA) ShowSymbol + 1.000000 0.000000 (GGT) ShowSymbol + 1.000000 0.000000 (GGG) ShowSymbol + 1.000000 0.000000 (GGC) ShowSymbol + 1.000000 0.000000 (GGA) ShowSymbol + 1.000000 0.000000 (GCT) ShowSymbol + 1.000000 0.000000 (GCG) ShowSymbol + 1.000000 0.000000 (GCC) ShowSymbol + 1.000000 0.000000 (GCA) ShowSymbol + 1.000000 0.000000 (GAG) ShowSymbol + 1.000000 0.000000 (CTT) ShowSymbol + 1.000000 0.000000 (CTG) ShowSymbol + 1.000000 0.000000 (CTC) ShowSymbol + 1.000000 0.000000 (CTA) ShowSymbol + 1.000000 0.000000 (CGT) ShowSymbol + 1.000000 0.000000 (CGG) ShowSymbol + 1.000000 0.000000 (CGC) ShowSymbol + 1.000000 0.000000 (CCT) ShowSymbol + 1.000000 0.000000 (CCG) ShowSymbol + 1.000000 0.000000 (CCC) ShowSymbol + 1.000000 0.000000 (CCA) ShowSymbol + 1.000000 0.000000 (CAT) ShowSymbol + 1.000000 0.000000 (CAG) ShowSymbol + 1.000000 0.000000 (CAC) ShowSymbol + 1.000000 0.000000 (CAA) ShowSymbol + 1.000000 0.000000 (ATC) ShowSymbol + 1.000000 0.000000 (ATA) ShowSymbol + 1.000000 0.000000 (AGT) ShowSymbol + 1.000000 0.000000 (AGC) ShowSymbol + 1.000000 0.000000 (ACT) ShowSymbol + 1.000000 0.000000 (ACG) ShowSymbol + 1.000000 0.000000 (ACC) ShowSymbol + 1.000000 0.000000 (ACA) ShowSymbol + 1.000000 0.018239 (TGC) ShowSymbol + 1.000000 0.018239 (GTG) ShowSymbol + 1.000000 0.018239 (GAT) ShowSymbol + 1.000000 0.018239 (GAC) ShowSymbol + 1.000000 0.018239 (GAA) ShowSymbol + 1.000000 0.018239 (CGA) ShowSymbol + 1.000000 0.018239 (AGG) ShowSymbol + 1.000000 0.036479 (TTG) ShowSymbol + 1.000000 0.036479 (TTA) ShowSymbol + 1.000000 0.036479 (TCT) ShowSymbol + 1.000000 0.036479 (ATG) ShowSymbol + 1.000000 0.036479 (AAC) ShowSymbol + 1.000000 0.054718 (ATT) ShowSymbol + 1.000000 0.054718 (AGA) ShowSymbol + 1.000000 0.054718 (AAG) ShowSymbol + 1.000000 0.072957 (AAT) ShowSymbol + 1.000000 0.091196 (AAA) ShowSymbol + 1.000000 0.109436 (TAA) ShowSymbol + 1.000000 0.145914 (TTT) ShowSymbol + 0.311195 0.311195 DrawErrorbar +EndStack + +(2) StartStack + 1.000000 0.000000 (TTG) ShowSymbol + 1.000000 0.000000 (TTA) ShowSymbol + 1.000000 0.000000 (TGG) ShowSymbol + 1.000000 0.000000 (TCT) ShowSymbol + 1.000000 0.000000 (TCG) ShowSymbol + 1.000000 0.000000 (TCC) ShowSymbol + 1.000000 0.000000 (TCA) ShowSymbol + 1.000000 0.000000 (TAG) ShowSymbol + 1.000000 0.000000 (TAC) ShowSymbol + 1.000000 0.000000 (TAA) ShowSymbol + 1.000000 0.000000 (GTT) ShowSymbol + 1.000000 0.000000 (GTG) ShowSymbol + 1.000000 0.000000 (GTC) ShowSymbol + 1.000000 0.000000 (GTA) ShowSymbol + 1.000000 0.000000 (GGG) ShowSymbol + 1.000000 0.000000 (GGA) ShowSymbol + 1.000000 0.000000 (GCT) ShowSymbol + 1.000000 0.000000 (GCG) ShowSymbol + 1.000000 0.000000 (GCC) ShowSymbol + 1.000000 0.000000 (GCA) ShowSymbol + 1.000000 0.000000 (GAT) ShowSymbol + 1.000000 0.000000 (GAG) ShowSymbol + 1.000000 0.000000 (GAC) ShowSymbol + 1.000000 0.000000 (GAA) ShowSymbol + 1.000000 0.000000 (CTT) ShowSymbol + 1.000000 0.000000 (CTG) ShowSymbol + 1.000000 0.000000 (CTA) ShowSymbol + 1.000000 0.000000 (CGG) ShowSymbol + 1.000000 0.000000 (CGC) ShowSymbol + 1.000000 0.000000 (CGA) ShowSymbol + 1.000000 0.000000 (CCG) ShowSymbol + 1.000000 0.000000 (CCC) ShowSymbol + 1.000000 0.000000 (CCA) ShowSymbol + 1.000000 0.000000 (CAT) ShowSymbol + 1.000000 0.000000 (CAG) ShowSymbol + 1.000000 0.000000 (CAC) ShowSymbol + 1.000000 0.000000 (CAA) ShowSymbol + 1.000000 0.000000 (ATT) ShowSymbol + 1.000000 0.000000 (ATG) ShowSymbol + 1.000000 0.000000 (ATC) ShowSymbol + 1.000000 0.000000 (ATA) ShowSymbol + 1.000000 0.000000 (AGT) ShowSymbol + 1.000000 0.000000 (AGG) ShowSymbol + 1.000000 0.000000 (AGC) ShowSymbol + 1.000000 0.000000 (AGA) ShowSymbol + 1.000000 0.000000 (ACT) ShowSymbol + 1.000000 0.000000 (ACG) ShowSymbol + 1.000000 0.000000 (ACC) ShowSymbol + 1.000000 0.000000 (ACA) ShowSymbol + 1.000000 0.000000 (AAT) ShowSymbol + 1.000000 0.000000 (AAG) ShowSymbol + 1.000000 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1.000000 0.000000 (TGC) ShowSymbol + 1.000000 0.000000 (TGA) ShowSymbol + 1.000000 0.000000 (TCT) ShowSymbol + 1.000000 0.000000 (TCC) ShowSymbol + 1.000000 0.000000 (TAC) ShowSymbol + 1.000000 0.000000 (TAA) ShowSymbol + 1.000000 0.000000 (GTT) ShowSymbol + 1.000000 0.000000 (GTA) ShowSymbol + 1.000000 0.000000 (GGT) ShowSymbol + 1.000000 0.000000 (GGG) ShowSymbol + 1.000000 0.000000 (GGC) ShowSymbol + 1.000000 0.000000 (GCT) ShowSymbol + 1.000000 0.000000 (GAC) ShowSymbol + 1.000000 0.000000 (GAA) ShowSymbol + 1.000000 0.000000 (CTT) ShowSymbol + 1.000000 0.000000 (CTA) ShowSymbol + 1.000000 0.000000 (CGC) ShowSymbol + 1.000000 0.000000 (CGA) ShowSymbol + 1.000000 0.000000 (CCT) ShowSymbol + 1.000000 0.000000 (CCG) ShowSymbol + 1.000000 0.000000 (CAG) ShowSymbol + 1.000000 0.000000 (CAC) ShowSymbol + 1.000000 0.000000 (ATC) ShowSymbol + 1.000000 0.000000 (ATA) ShowSymbol + 1.000000 0.000000 (AGT) ShowSymbol + 1.000000 0.000000 (AGG) ShowSymbol + 1.000000 0.000000 (AGA) ShowSymbol + 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1.000000 0.029127 (TCA) ShowSymbol + 1.000000 0.029127 (GTG) ShowSymbol + 1.000000 0.029127 (GCG) ShowSymbol + 1.000000 0.029127 (CAT) ShowSymbol + 1.000000 0.043690 (CCA) ShowSymbol + 1.000000 0.043690 (CAA) ShowSymbol + 1.000000 0.043690 (ATT) ShowSymbol + 1.000000 0.043690 (ACA) ShowSymbol + 1.000000 0.072817 (CTG) ShowSymbol + 0.421733 0.421733 DrawErrorbar +EndStack + +(5) StartStack + 1.000000 0.000000 (TTG) ShowSymbol + 1.000000 0.000000 (TTC) ShowSymbol + 1.000000 0.000000 (TTA) ShowSymbol + 1.000000 0.000000 (TGG) ShowSymbol + 1.000000 0.000000 (TGA) ShowSymbol + 1.000000 0.000000 (TCC) ShowSymbol + 1.000000 0.000000 (TCA) ShowSymbol + 1.000000 0.000000 (TAG) ShowSymbol + 1.000000 0.000000 (TAC) ShowSymbol + 1.000000 0.000000 (TAA) ShowSymbol + 1.000000 0.000000 (GTC) ShowSymbol + 1.000000 0.000000 (GTA) ShowSymbol + 1.000000 0.000000 (GGG) ShowSymbol + 1.000000 0.000000 (GGC) ShowSymbol + 1.000000 0.000000 (GGA) ShowSymbol + 1.000000 0.000000 (GCC) ShowSymbol + 1.000000 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1.000000 0.017469 (TCT) ShowSymbol + 1.000000 0.017469 (TCA) ShowSymbol + 1.000000 0.017469 (GGA) ShowSymbol + 1.000000 0.017469 (GCT) ShowSymbol + 1.000000 0.017469 (GAA) ShowSymbol + 1.000000 0.017469 (ACA) ShowSymbol + 1.000000 0.034937 (TTT) ShowSymbol + 1.000000 0.034937 (CAT) ShowSymbol + 1.000000 0.034937 (CAA) ShowSymbol + 1.000000 0.034937 (AGT) ShowSymbol + 1.000000 0.052406 (GTT) ShowSymbol + 1.000000 0.052406 (AGA) ShowSymbol + 1.000000 0.052406 (AAT) ShowSymbol + 1.000000 0.069875 (AAA) ShowSymbol + 1.000000 0.087344 (ATA) ShowSymbol + 1.000000 0.087344 (ACT) ShowSymbol + 1.000000 0.174687 (ATT) ShowSymbol + 0.295737 0.295737 DrawErrorbar +EndStack + +EndLine + +EndLogo + + +%%EOF +
--- a/weblogolib/__init__.py Mon Jan 30 08:17:57 2012 -0500 +++ b/weblogolib/__init__.py Mon Jan 30 21:17:50 2012 -0500 @@ -983,11 +983,20 @@ prior = weight * equiprobable_distribution(len(alphabet)) elif comp.lower() == 'escherichiacoli' : - 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}" + 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}" + else: + 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}" elif comp.lower() == 'homosapiens' : - composition="{'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': 1.2672, 'TAT': 0.7807999999999999, 'GGT': 0.6912, 'TGT': 0.6784, 'CGA': 0.3968, 'CAG': 2.1888, 'TCT': 0.9728, 'GAT': 1.3952, 'CGG': 0.7296, 'TTT': 1.1264, 'TGC': 0.8064, 'GGG': 1.056, 'TAG': 0.0512, 'GGA': 1.056, 'TAA': 0.064, 'GGC': 1.4208, 'TAC': 0.9792000000000001, 'TTC': 1.2992000000000001, 'TCG': 0.2816, 'TTA': 0.4928, 'TTG': 0.8256, 'TCC': 1.1328, 'ACC': 1.2096, 'TCA': 0.7807999999999999, 'GCA': 1.0112, 'GTA': 0.45439999999999997, 'GCC': 1.7728, 'GTC': 0.928, 'GCG': 0.4736, 'GTG': 1.7984, 'GAG': 2.5344, 'GTT': 0.704, 'GCT': 1.1776, 'TGA': 0.1024, 'GAC': 1.6064, 'CGT': 0.288, 'TGG': 0.8448, 'GAA': 1.856, 'CGC': 0.6656}" - elif comp.lower() == 'saccharomycescerevisiae' : - 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}" + if(altype=="codonsT"): + composition="{'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': 1.2672, 'TAT': 0.7807999999999999, 'GGT': 0.6912, 'TGT': 0.6784, 'CGA': 0.3968, 'CAG': 2.1888, 'TCT': 0.9728, 'GAT': 1.3952, 'CGG': 0.7296, 'TTT': 1.1264, 'TGC': 0.8064, 'GGG': 1.056, 'TAG': 0.0512, 'GGA': 1.056, 'TAA': 0.064, 'GGC': 1.4208, 'TAC': 0.9792000000000001, 'TTC': 1.2992000000000001, 'TCG': 0.2816, 'TTA': 0.4928, 'TTG': 0.8256, 'TCC': 1.1328, 'ACC': 1.2096, 'TCA': 0.7807999999999999, 'GCA': 1.0112, 'GTA': 0.45439999999999997, 'GCC': 1.7728, 'GTC': 0.928, 'GCG': 0.4736, 'GTG': 1.7984, 'GAG': 2.5344, 'GTT': 0.704, 'GCT': 1.1776, 'TGA': 0.1024, 'GAC': 1.6064, 'CGT': 0.288, 'TGG': 0.8448, 'GAA': 1.856, 'CGC': 0.6656}" + else: + composition="{'CUU': 0.8448, '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}" + elif comp.lower() == 'saccharomycescerevisiae' : + if(altype=="codonsT"): + 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}" + else: + 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}" elif comp.lower() == 'auto' or comp.lower() == 'automatic': if alphabet == unambiguous_protein_alphabet : prior = weight * asarray(aa_composition, float64) @@ -1002,7 +1011,7 @@ elif isfloat(comp) : prior = weight * base_distribution( float(comp)*100. ) - elif composition[0] == '{' and composition[-1] == '}' : + if composition[0] == '{' and composition[-1] == '}' : explicit = composition[1: -1] explicit = explicit.replace(',',' ').replace("'", ' ').replace('"',' ').replace(':', ' ').split()