| Previous changeset 7:8d676bbd1f2d (2012-01-16) Next changeset 9:f3462128e87c (2012-01-30) |
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Commit message:
Uploaded |
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modified:
Codonlogo.xml README.txt weblogolib/__init__.py weblogolib/template.eps |
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added:
README.txt~ examples/Escherichiacoli.txt examples/Galaxy-Workflow-Figure.ga examples/Galaxy53-[_2_Frame_output.pdf](1).pdf examples/Galaxy54-[_1_Frame_output.pdf].pdf examples/Galaxy55-[0_Frame_output.pdf].pdf examples/Homosapiens.txt examples/Saccharomycescerevisiae.txt examples/alignment_real.txt weblogolib/.__init__.py.kate-swp |
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removed:
examplepriorfile.txt |
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| diff -r 8d676bbd1f2d -r 5149eb3a89c2 Codonlogo.xml --- a/Codonlogo.xml Mon Jan 16 07:03:36 2012 -0500 +++ b/Codonlogo.xml Fri Jan 20 09:03:40 2012 -0500 |
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| @@ -1,27 +1,37 @@ <tool id="codonlogo" name="Codon Logo" version="3"> <description>generator for fasta (eg Clustal alignments)</description> - <command interpreter="python -W ignore::DeprecationWarning"> - codonlogo -F $outformat -s $size -f $input -o $output -t "$logoname" -m $frame -n $stacks -X $showxaxis --show-yaxis $showyaxis --errorbars $errorbars + <command interpreter="/usr/tmp/bin/python2.7 -W ignore::DeprecationWarning"> + codonlogo -F $outformat -s $size -f $input -o $output -t "$logoname" -m $frame -n $stacks -X $showxaxis --show-yaxis $showyaxis --errorbars $errorbars -G $strict --fineprint "$fineprint" --stack-width $stackwidth --stack-height $stackheight --box $box --resolution $resolution --scale-width $scalewidth #if str($ylabel) != '' - -x $xlabel + -x "$xlabel" #end if #if str( $ylabel) != '' - -y $ylabel + -y "$ylabel" #end if - #if $range.mode == 'part' + + #if str($range.mode) == 'part' -l "$range.seqstart" -u "$range.seqend" #end if - #if $comp.mode == 'equiprobable' + #if str($comp.mode) == 'equiprobable' --composition 'equiprobable' #end if - #if $comp.mode == 'none' + #if str($comp.mode) == 'none' --composition 'none' #end if - #if $comp.mode == 'file' + #if str($comp.mode) == 'file' -R $compfile #end if + #if str($comp.mode) == 'Escherichiacoli' + -R Escherichiacoli.txt + #end if + #if str($comp.mode) == 'Saccharomycescerevisiae' + -R Saccharomycescerevisiae.txt + #end if + #if str($comp.mode) == 'Homosapiens' + -R Homosapiens.txt + #end if #if $colours.colour == 'part' @@ -322,7 +332,7 @@ </command> <inputs> <page> - <param format="fasta" name="input" type="data" label="txt" /> + <param format="text" name="input" type="data" label="Input file.(must be an aligned fasta file of sequences the same length, recommended to use sequences aligned by codon)" /> <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="" /> @@ -334,13 +344,15 @@ <option value="eps">EPS</option> <option value="txt">Text (shows the detailed calculations for each position - no image)</option> </param> + <param name="resolution" size="5" type="integer" value="96" label="Bitmap resolution in dots per inch (DPI).For high quality printable PNG this should be set to 600" /> + <param name="frame" type="select" label="Frame to view the alignment. If reverse complement is selected then codonlogo will read from the last symbol in the sequences backwards and replace each base with it's complement." > <option value="0" selected="True">0</option> <option value="1">+1</option> - <option value="2">-1</option> + <option value="2">+2</option> <option value="3">reverse complement 0</option> <option value="4">reverse complement +1</option> - <option value="5">reverse complement -1</option> + <option value="5">reverse complement +2</option> </param> <param name="stacks" size="5" type="integer" value="20" label="Number of stacks per line, default 20" /> <param name="showxaxis" type="select" display="radio" label="Display sequence numbers along x-axis?" > @@ -350,9 +362,15 @@ <param name="xlabel" label="X-axis label" type="text" size="50" value="" /> <param name="ylabel" label="Y-axis label" type="text" size="50" value="" /> - <param name="fineprint" label="The fine print." type="text" size="50" value="CodonLogo 1.0" /> + <param name="fineprint" label="The fine print." type="text" size="50" value="CodonLogo 1.1" /> + + <param name="stackwidth" size="5" type="float" value="40.0" label="Width of a logo stack" /> - + <param name="stackheight" size="5" type="integer" value="100" label="height of a logo stack" /> + <param name="box" type="select" display="radio" label="Draw boxes around symbols?" > + <option value="True" >Yes</option> + <option value="False" selected="True">No</option> + </param> <param name="showyaxis" type="select" display="radio" label="Display entropy scale along y-axis?" > <option value="True" selected="True">Yes</option> <option value="False">No</option> @@ -361,6 +379,14 @@ <option value="True" selected="True">Yes</option> <option value="False">No</option> </param> + <param name="scalewidth" type="select" display="radio" label="Scale the visible stack width by the fraction of symbols in the column?" > + <option value="True" selected="True">Yes</option> + <option value="False">No</option> + </param> + <param name="strict" type="select" display="radio" label="Allow gaps which are not in groups of 3/ allow codons with ambiguous nucleotides." > + <option value="False" selected="True">Yes</option> + <option value="True" >No</option> + </param> <conditional name="range"> <param name="mode" type="select" label="Include entire sequence (default) or specify a subsequence range to use"> <option value="complete" selected="true">complete sequence</option> @@ -369,10 +395,10 @@ <when value="complete"> </when> <when value="part"> - <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!" - label="Index (eg 1=first letter) of the start of the sequence range to include in the logo"> + <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying codon numbers outside the sequence lengths will cause unpredictable but bad consequences!" + label="Index_start (eg 1=first codon) of the start of the sequence range to include in the logo"> </param> - <param name="seqend" size="5" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" > + <param name="seqend" size="5" type="integer" value="99999" label="Index_end (eg 75=75th codon) of the end of the sequence range to include in the logo" > </param> </when> </conditional> @@ -381,6 +407,9 @@ <option value="equiprobable" >equiprobable</option> <option value="none" >none</option> +<!-- <option value="Escherichiacoli" >Escherichiacoli</option> + <option value="Homosapiens" >Homosapiens</option> + <option value="Saccharomycescerevisiae" >Saccharomycescerevisiae</option>--> <option value="file">from file</option> </param> |
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| diff -r 8d676bbd1f2d -r 5149eb3a89c2 README.txt --- a/README.txt Mon Jan 16 07:03:36 2012 -0500 +++ b/README.txt Fri Jan 20 09:03:40 2012 -0500 |
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| @@ -1,38 +1,51 @@ - -CodonLogo (http://recode.ucc.ie/CodonLogo) is a tool for creating sequence -logos from biological sequence alignments. It can be run on the command line, -as a standalone webserver or as a CGI webapp. - - -For help on the command line interface run - ./codonlogo --help - -To build a simple logo run - ./codonlogo < cap.fa > logo.eps - - -To run as a standalone webserver at localhost:8080 - ./codonlogo --server - - -An example file of probabilities is included, examplepriorfile.txt -It can be used with the following command. - - ./codonlogo --prior examplepriorfile.txt < cap.fa > logo.eps - - -There is a known issue with GPL Ghostscript 9.04 which affects some users which may cause ghostscript to segfault. -This is not believed to be a problem with CodonLogo. -This is being investigated. if you encounter this problem it's recommended to downgrade to version 9.01 or earlier of ghostscript. - - - --- Distribution and Modification -- -This package is distributed under the new BSD Open Source License. -Please see the LICENSE.txt file for details on copyright and licensing. -The CodonLogo source code can be downloaded from -http://recode.ucc.ie/CodonLogo - -CodonLogo requires Python 2.6 or 2.7, the corebio python toolkit for -computational biology (http://code.google.com/p/corebio), and the python -array package 'numpy' (http://www.scipy.org/Download) + +CodonLogo (http://recode.ucc.ie/CodonLogo) is a tool for creating sequence +logos from biological sequence alignments. It can be run from the command line as a standalone webserver or as a CGI webapp. + + +For help on the command line interface run + ./codonlogo --help + +To build a simple logo run + ./codonlogo < cap.fa > logo.eps + + +To run as a standalone webserver at localhost:8080 + ./codonlogo --server + + +An example file of probabilities is included, examplepriorfile.txt +It can be used with the following command. + + ./codonlogo --prior ./examples/Escherichiacoli.txt < cap.fa > logo.eps + + +examplepriorfile contains the frequencies for codons in human CDS regions. + + +KNOWN ISSUES: + +There is a known issue with GPL Ghostscript 9.04 which affects some users which may cause ghostscript to segfault or prevent codonlogos from being generated in anything other than eps format. + +This is believed to be an issue with ghostscript and a bug report has been submitted to the ghostscript mailing list. +This is being investigated. if you encounter this problem it's recommended to downgrade to version 9.01 of ghostscript or earlier . + + + +For converting files to a suitable format the following sites can be used: + +http://genome.nci.nih.gov/tools/reformat.html +http://www-bimas.cit.nih.gov/molbio/readseq/ + + + + +-- Distribution and Modification -- +This package is distributed under the new BSD Open Source License. +Please see the LICENSE.txt file for details on copyright and licensing. +The CodonLogo source code can be downloaded from +http://recode.ucc.ie/CodonLogo + +CodonLogo requires Python 2.6 or 2.7, the corebio python toolkit for +computational biology (http://code.google.com/p/corebio), and the python +array package 'numpy' (http://www.scipy.org/Download) |
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| diff -r 8d676bbd1f2d -r 5149eb3a89c2 README.txt~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt~ Fri Jan 20 09:03:40 2012 -0500 |
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| @@ -0,0 +1,47 @@ + +CodonLogo (http://recode.ucc.ie/CodonLogo) is a tool for creating sequence +logos from biological sequence alignments. It can be run on the command line, +as a standalone webserver or as a CGI webapp. + + +For help on the command line interface run + ./codonlogo --help + +To build a simple logo run + ./codonlogo < cap.fa > logo.eps + + +To run as a standalone webserver at localhost:8080 + ./codonlogo --server + + +An example file of probabilities is included, examplepriorfile.txt +It can be used with the following command. + + ./codonlogo --prior examplepriorfile.txt < cap.fa > logo.eps + + +examplepriorfile contains the frequencies for codons in human CDS regions. + + +There is a known issue with GPL Ghostscript 9.04 which affects some users which may cause ghostscript to segfault. +This is not believed to be a problem with CodonLogo. +This is being investigated. if you encounter this problem it's recommended to downgrade to version 9.01 or earlier of ghostscript. + +For converting files to a suitable format the following sites can be used: + +http://genome.nci.nih.gov/tools/reformat.html +http://www-bimas.cit.nih.gov/molbio/readseq/ + + + + +-- Distribution and Modification -- +This package is distributed under the new BSD Open Source License. +Please see the LICENSE.txt file for details on copyright and licensing. +The CodonLogo source code can be downloaded from +http://recode.ucc.ie/CodonLogo + +CodonLogo requires Python 2.6 or 2.7, the corebio python toolkit for +computational biology (http://code.google.com/p/corebio), and the python +array package 'numpy' (http://www.scipy.org/Download) |
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| diff -r 8d676bbd1f2d -r 5149eb3a89c2 examplepriorfile.txt --- a/examplepriorfile.txt Mon Jan 16 07:03:36 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,64 +0,0 @@ -AAA 1 -AAC 1.5 -AAG 0.5 -AAT 1 -ACA 1 -ACC 1 -ACG 1 -ACT 1 -AGA 1 -AGC 1 -AGG 1 -AGT 1 -ATA 1 -ATC 1 -ATG 1 -ATT 1 -CAA 1 -CAC 1 -CAG 1 -CAT 1 -CCA 1 -CCC 1 -CCG 1 -CCT 1 -CGA 1 -CGC 1 -CGG 1 -CGT 1 -CTA 1 -CTC 1 -CTG 1 -CTT 1 -GAA 1 -GAC 1 -GAG 1 -GAT 1 -GCA 1 -GCC 1 -GCG 1 -GCT 1 -GGA 1 -GGC 1 -GGG 1 -GGT 1 -GTA 1 -GTC 1 -GTG 1 -GTT 1 -TAA 1 -TAC 1 -TAG 1 -TAT 1 -TCA 1 -TCC 1 -TCG 1 -TCT 1 -TGA 1 -TGC 1 -TGG 1 -TGT 1 -TTA 1 -TTC 1 -TTG 1 -TTT 1 |
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| diff -r 8d676bbd1f2d -r 5149eb3a89c2 examples/Escherichiacoli.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/examples/Escherichiacoli.txt Fri Jan 20 09:03:40 2012 -0500 |
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| @@ -0,0 +1,64 @@ +UUU 19.7 +UUC 15 +UUA 15.2 +UUG 11.9 +CUU 11.9 +CUC 10.5 +CUA 5.3 +CUG 46.9 +AUU 30.5 +AUC 18.2 +AUA 3.7 +AUG 24.8 +GUU 16.8 +GUC 11.7 +GUA 11.5 +GUG 26.4 +UCU 5.7 +UCC 5.5 +UCA 7.8 +UCG 8 +CCU 8.4 +CCC 6.4 +CCA 6.6 +CCG 26.7 +ACU 8 +ACC 22.8 +ACA 6.4 +ACG 11.5 +GCU 10.7 +GCC 31.6 +GCA 21.1 +GCG 38.5 +UAU 16.8 +UAC 14.6 +UAA 1.8 +UAG 0 +CAU 15.8 +CAC 13.1 +CAA 12.1 +CAG 27.7 +AAU 21.9 +AAC 24.4 +AAA 33.2 +AAG 12.1 +GAU 37.9 +GAC 20.5 +GAA 43.7 +GAG 18.4 +UGU 5.9 +UGC 8 +UGA 1 +UGG 10.7 +CGU 21.1 +CGC 26 +CGA 4.3 +CGG 4.1 +AGU 7.2 +AGC 16.6 +AGA 1.4 +AGG 1.6 +GGU 21.3 +GGC 33.4 +GGA 9.2 +GGG 8.6 \ No newline at end of file |
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| diff -r 8d676bbd1f2d -r 5149eb3a89c2 examples/Galaxy-Workflow-Figure.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/examples/Galaxy-Workflow-Figure.ga Fri Jan 20 09:03:40 2012 -0500 |
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| @@ -0,0 +1,118 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "Generates part B", + "format-version": "0.1", + "name": "Figure", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input Dataset" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 197, + "top": 384 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Input Dataset\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": { + "input": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "Codon Logo", + "outputs": [ + { + "name": "output", + "type": "pdf" + } + ], + "position": { + "left": 580, + "top": 228 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "codonlogo", + "tool_state": "{\"outformat\": \"\\\"pdf\\\"\", \"frame\": \"\\\"0\\\"\", \"size\": \"\\\"large\\\"\", \"__page__\": 0, \"colours\": \"{\\\"colour\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"strict\": \"\\\"False\\\"\", \"logoname\": \"\\\"0 Frame\\\"\", \"ylabel\": \"\\\"\\\"\", \"input\": \"null\", \"stackheight\": \"\\\"100\\\"\", \"scalewidth\": \"\\\"True\\\"\", \"showyaxis\": \"\\\"True\\\"\", \"comp\": \"{\\\"mode\\\": \\\"equiprobable\\\", \\\"__current_case__\\\": 1}\", \"showxaxis\": \"\\\"True\\\"\", \"stackwidth\": \"\\\"40.0\\\"\", \"box\": \"\\\"False\\\"\", \"fineprint\": \"\\\"\\\"\", \"range\": \"{\\\"seqend\\\": \\\"16\\\", \\\"mode\\\": \\\"part\\\", \\\"__current_case__\\\": 1, \\\"seqstart\\\": \\\"6\\\"}\", \"xlabel\": \"\\\"\\\"\", \"errorbars\": \"\\\"True\\\"\", \"resolution\": \"\\\"96\\\"\", \"stacks\": \"\\\"20\\\"\"}", + "tool_version": "3", + "type": "tool", + "user_outputs": [] + }, + "2": { + "annotation": "", + "id": 2, + "input_connections": { + "input": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "Codon Logo", + "outputs": [ + { + "name": "output", + "type": "pdf" + } + ], + "position": { + "left": 580, + "top": 360 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "codonlogo", + "tool_state": "{\"outformat\": \"\\\"pdf\\\"\", \"frame\": \"\\\"1\\\"\", \"size\": \"\\\"large\\\"\", \"__page__\": 0, \"colours\": \"{\\\"colour\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"strict\": \"\\\"False\\\"\", \"logoname\": \"\\\"+1 Frame\\\"\", \"ylabel\": \"\\\"\\\"\", \"input\": \"null\", \"stackheight\": \"\\\"100\\\"\", \"scalewidth\": \"\\\"True\\\"\", \"showyaxis\": \"\\\"True\\\"\", \"comp\": \"{\\\"mode\\\": \\\"equiprobable\\\", \\\"__current_case__\\\": 1}\", \"showxaxis\": \"\\\"True\\\"\", \"stackwidth\": \"\\\"40.0\\\"\", \"box\": \"\\\"False\\\"\", \"fineprint\": \"\\\"\\\"\", \"range\": \"{\\\"seqend\\\": \\\"16\\\", \\\"mode\\\": \\\"part\\\", \\\"__current_case__\\\": 1, \\\"seqstart\\\": \\\"6\\\"}\", \"xlabel\": \"\\\"\\\"\", \"errorbars\": \"\\\"True\\\"\", \"resolution\": \"\\\"96\\\"\", \"stacks\": \"\\\"20\\\"\"}", + "tool_version": "3", + "type": "tool", + "user_outputs": [] + }, + "3": { + "annotation": "", + "id": 3, + "input_connections": { + "input": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "Codon Logo", + "outputs": [ + { + "name": "output", + "type": "pdf" + } + ], + "position": { + "left": 580, + "top": 493 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "codonlogo", + "tool_state": "{\"outformat\": \"\\\"pdf\\\"\", \"frame\": \"\\\"2\\\"\", \"size\": \"\\\"large\\\"\", \"__page__\": 0, \"colours\": \"{\\\"colour\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"strict\": \"\\\"False\\\"\", \"logoname\": \"\\\"+2 Frame\\\"\", \"ylabel\": \"\\\"\\\"\", \"input\": \"null\", \"stackheight\": \"\\\"100\\\"\", \"scalewidth\": \"\\\"True\\\"\", \"showyaxis\": \"\\\"True\\\"\", \"comp\": \"{\\\"mode\\\": \\\"equiprobable\\\", \\\"__current_case__\\\": 1}\", \"showxaxis\": \"\\\"True\\\"\", \"stackwidth\": \"\\\"40.0\\\"\", \"box\": \"\\\"False\\\"\", \"fineprint\": \"\\\"\\\"\", \"range\": \"{\\\"seqend\\\": \\\"16\\\", \\\"mode\\\": \\\"part\\\", \\\"__current_case__\\\": 1, \\\"seqstart\\\": \\\"6\\\"}\", \"xlabel\": \"\\\"\\\"\", \"errorbars\": \"\\\"True\\\"\", \"resolution\": \"\\\"96\\\"\", \"stacks\": \"\\\"20\\\"\"}", + "tool_version": "3", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file |
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| diff -r 8d676bbd1f2d -r 5149eb3a89c2 examples/Homosapiens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/examples/Homosapiens.txt Fri Jan 20 09:03:40 2012 -0500 |
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| @@ -0,0 +1,64 @@ +UUU 17.6 +UUC 20.3 +UUA 7.7 +UUG 12.9 +CUU 13.2 +CUC 19.6 +CUA 7.2 +CUG 39.6 +AUU 16 +AUC 20.8 +AUA 7.5 +AUG 22 +GUU 11 +GUC 14.5 +GUA 7.1 +GUG 28.1 +UCU 15.2 +UCC 17.7 +UCA 12.2 +UCG 4.4 +CCU 17.5 +CCC 19.8 +CCA 16.9 +CCG 6.9 +ACU 13.1 +ACC 18.9 +ACA 15.1 +ACG 6.1 +GCU 18.4 +GCC 27.7 +GCA 15.8 +GCG 7.4 +UAU 12.2 +UAC 15.3 +UAA 1 +UAG 0.8 +CAU 10.9 +CAC 15.1 +CAA 12.3 +CAG 34.2 +AAU 17 +AAC 19.1 +AAA 24.4 +AAG 31.9 +GAU 21.8 +GAC 25.1 +GAA 29 +GAG 39.6 +UGU 10.6 +UGC 12.6 +UGA 1.6 +UGG 13.2 +CGU 4.5 +CGC 10.4 +CGA 6.2 +CGG 11.4 +AGU 12.1 +AGC 19.5 +AGA 12.2 +AGG 12 +GGU 10.8 +GGC 22.2 +GGA 16.5 +GGG 16.5 \ No newline at end of file |
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| diff -r 8d676bbd1f2d -r 5149eb3a89c2 examples/Saccharomycescerevisiae.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/examples/Saccharomycescerevisiae.txt Fri Jan 20 09:03:40 2012 -0500 |
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| @@ -0,0 +1,64 @@ +UUU 26.1 +UUC 18.4 +UUA 26.2 +UUG 27.2 +CUU 12.3 +CUC 5.4 +CUA 13.4 +CUG 10.5 +AUU 30.1 +AUC 17.2 +AUA 17.8 +AUG 20.9 +GUU 22.1 +GUC 11.8 +GUA 11.8 +GUG 10.8 +UCU 23.5 +UCC 14.2 +UCA 18.7 +UCG 8.6 +CCU 13.5 +CCC 6.8 +CCA 18.3 +CCG 5.3 +ACU 20.3 +ACC 12.7 +ACA 17.8 +ACG 8 +GCU 21.2 +GCC 12.6 +GCA 16.2 +GCG 6.2 +UAU 18.8 +UAC 14.8 +UAA 1.1 +UAG 0.5 +CAU 13.6 +CAC 7.8 +CAA 27.3 +CAG 12.1 +AAU 35.7 +AAC 24.8 +AAA 41.9 +AAG 30.8 +GAU 37.6 +GAC 20.2 +GAA 45.6 +GAG 19.2 +UGU 8.1 +UGC 4.8 +UGA 0.7 +UGG 10.4 +CGU 6.4 +CGC 2.6 +CGA 3 +CGG 1.7 +AGU 14.2 +AGC 9.8 +AGA 21.3 +AGG 9.2 +GGU 23.9 +GGC 9.8 +GGA 10.9 +GGG 6 \ No newline at end of file |
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| diff -r 8d676bbd1f2d -r 5149eb3a89c2 examples/alignment_real.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/examples/alignment_real.txt Fri Jan 20 09:03:40 2012 -0500 |
| b |
| b'@@ -0,0 +1,857 @@\n+GATAATCTGGCGCTGAAGGAACTGCTCTCAAAAAACTTCTGACGCCCGAGGTTAAGCGGC\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GACATGGAAGCGCTGAAGGTGGTGGTCAAGGGAAAGCCCTGAGCCCACAAGCCAAGCGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GACAAGCACATGCTCCAGGAGGTCCTTCGAAAAAAATTCTAAGGCCCGCGGCGTTGCGAC\n+GACAAGGCGGCGCTTCAGGATCTGCTAAGCCGAAAGTAGTCAGCCCGCAGGCCAAACGCG\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATAAGGAAATGCTGCAGGATGTCATCCGAAAAAAGTTCTGAGGCCGCTGCAGAAGCGTG\n+GAAAACCATGCATTGAAGGATGTCATCGCAAAAAAGCTGTAGACCCGGCGCATAAGCGCC\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATATGGAAGCGTTGAAGGTCGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+GACAAGGTCATGCTGCAGGATGTTCTGAGAAAAAAGCTCTAAGGCCGGCGCAGCGCAAAG\n+GACATGGAAGCGCTGAAGGTGGTGGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAGCGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GACAAAGAGATGCTGCAGGAGGTTATCAAAAAAAAGTTCTAAGGCCGGCGCAGAAGCGCG\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+CTCGACAATGCTGCCTTGAAAGACCTTTTGGGAAAGAAGTGGTGACGCCCGCGGCCAAGC\n+CTCGACAACGCCGCGTTGAAAGACCTTTTGGGAAAGAAGTGGTGACGCCCGCAGCCCAGC\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+AGCACCGATCTCCTGAAGGAAGCCCTCGCAAAAAAATGGTGAGGCCATCGCAACGTCGCG\n+CTCGACAACGCCGCGTTGAAAGACCTTTTGGGAAAGAAGTGGTGACGCCCGCAGCCCAGC\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATAATCAACTTCTTAAAGATCTCTTCACAAAAAAAGGCTGGGCCCTGCCACCCAAAGAC\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+AAATCAGATATCCTACAGGATGCCATTTCAAAAAAGTGGTAGCGCCCTCTAGGCGCAAAG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+AGTACCGACCTGCTGAAGGAAGCGCTCGCAAAAAAATGGTGAGGCCATCTCAGCGACGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATAACCAAATACTCAAAGAGATTTTCGTAAAAAAGGGCTGGGCTCTGCCGCAAAAAGGG\n+GACGTGGCCACGCTGCGTGAGGCGCTGGGAAAAAACTTCTGACGCCCGGCGCACGGAGAA\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+AGTACCGACCTGCTGAAGGAAGCGCTCGCAAAAAAATGGTGAGGCCATCTCAGCGACGCG\n+AAGGCCGAGATCGTGACGGAGACGCTTGAAAAAAAGTGGTGAGGCCATCTCGCCGCCGCG\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+GATATGGAAGCGTTGAAGGTCGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+GAAAATAAAGCAATGAAGGACTTAATAGAAAAAAAGCTCTAAGGCCGCAGGAAAGACGTG\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+GAGAACCGGGCACTGAAAGACGTTATCGAAAAAAAGCTTTAAAACCAGCCTGTAAGCGTG\n+GAAAACCATGCATTGAAGGATGTCATCGCAAAAAAACTGTAGACCCGGCGCACAAGCGCC\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+GAATGCCGGGCGCTGAAAGACGTCATCGAAAAAAAGCTTTAAAACCAGCGATAAAGCGTG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GACAAAGAGATGCTGCAGGAGGTTATCAAAAAAAAGTTCTAAGGCCGGCGCAGAAGCGCG\n+AAGGCCGAGATCGTGACGGAGGCGCTCGAAAAAAAGTGGTGAGGCCATCTCGCCGCCGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GACAAAGCGGCG'..b'AAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GACAAGGTCATGCTGCAGGATGTTCTGAGAAAAAAGCTCTAAGGCCGGCGCAGCGCAAAG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GAGAACCGGGCGCTGAAAGACGTTATCGAAAAAAAGCTTTAAAACCAGCCTTTAAGCGTG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATAATCAACTTCTTAAAGATCTCTTCACAAAAAAAGGCTGGGCCCTGCCACCCAAAGAC\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+GATAAGGAGGCGCTTCAGGTGGCTCTGGGGCGAAAGTACTGACGACAGGCCAGAAGCGGG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATAACGCCGCGCTGAAGGACCTGCTGTCTCGAAAGTAGCAAGCCCGCAGGCCAAGCGCG\n+CTCGACAATGCTGCCTTGAAAGACCTTTTGGGAAAGAAGTGGTGACGCCCGCGGCCAAGC\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATCACAAAATCCTGAAGGATATTGTTGAAAAAAAGCTGTGAAGCCAACTGTGCGTCGGG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+GAAAACGAGGCATTGAAGGATGTCATCACAAAAAAGCTCTGAGGCCAGCCGAGAAGCGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+GACGTGGCCACGCTGCGTGAGGCGCTGGGAAAAAACTTCTGACGCCCGGCGCACGGAGAA\n+GATAAGGAGGCACTTCAGGTGGCTCTGGGGCGAAAGTACTGACGACAGACCAGAAGCGGG\n+GACATGGAAGCGCTGAAGGTGGTGGTCAAGGGAAAGCCCTGAGCCCACAAGCCAAGCGCG\n+AGTACCGACCTGCTGAAGGAAGCGCTCGCAAAAAAATGGTGAGGCCATCTCAGCGACGCG\n+GAACATAAGATCCTCAAAGATCTCGTCGAAAAAAAGCTCTGAAGCCAGCGGTCAGGCGTG\n+GAAAACCATGCATTGAAGGATGTCATCGCAAAAAAGCTGTAGACCCGGCGCATAAGCGCC\n+GACAAAGCGGCGTTGAAGGATCTTCTGGCAAAAAAGTTCTGACGCCCGCCGCGCAGCGGG\n+GATATGGAAGCGTTGAAGGTCGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATCATGAAATTCTTAAGGATGTTGTTTCAAAAAAACTTTAACGGTGCCTGAGAAGCGTG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+AGTACCGACCTGCTGAAGGAAGCGCTCGCAAAAAAATGGTGAGGCCATCTCAGCGACGCG\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+GACGTGGCCACGCTGCGTGAGGCGCTGGGAAAAAACTTCTGACGCCCGGCGCACGGAGAA\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GAGAACACGGCCCTGAAGGACGTGATCACAAAAAAGCTCTGAGCCCGGACGAGAAGCGCC\n+GAAAACCGTGCTTTGAAGGATCTGATCGAAAAAAAGCTTTAAGGCCGACTGGGAAACGCG\n+ATGCACCATGCGTTGAAGGACGTCGTTGACCGAAAGCTCTGACCCCGCAGCGTCGGATTG\n+ACTGCCGAAGTACTTCGTGAGGCGATGGCAAAAAAATGGTGAGGCCATCTCAACGCCGGG\n+AAGGCTGAGATCGTCAAGGAAGCCCTCGAAAAAAAGTGGTGAAGCCATCTCGTCGGCGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATAATCAACTTCTTAAAGATCTCTTCACAAAAAAAGGCTGGGCCCTGCCACCCAAAGAC\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GACAAGCACATCCTGCAGGACGTGCTCGCAAAAAAGCTCTGACGCCTGCTCGGCGACGCG\n+CAGAACGATCTGCTGAAGGAAGCCCTTGGAAAAAAGTGGTGAGGCCGTCTCAAAGACGCG\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+CAGGCCGATTTGCTGAAGGAGGCTCTCGGAAAAAAATGACGCGGCCATCTCAACGCCGCG\n+AGTACCGACCTGCTGAAGGAAGCGCTCGCAAAAAAATGGTGAGGCCATCTCAGCGACGCG\n+GACAATGTCCTGCTGAAGGAAGTCCTCGGAAAAAAATGGTGACGCCCACGGCGTTGCGGG\n+GACGTGGCCACGCTGCGTGAGGCGCTGGGAAAAAACTTCTGACGCCCGGCGCACGGAGAA\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+AAGGCAGAGATCGTCGCGGAGGCACTCGCAAAAAAGGACTGAGGCCATCTCGCCGGCGCG\n+GAGCACGAGGTCTTGAAGGACATCATAGCAAAAAAGCTCTGAGGCCAACCGAGAAGCGGG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+GATATGGAAGCGTTGAAGGTTGTCGTCAAGGGAAAGCCCTGAGCCCGCAAGCCAAACGCG\n+CAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGG\n+AAAGCCGAGATTATTCAGGAAGCCATGATAAAAAAGTGGTAAAGCCTGCTCAGCGTCGAC\n' |
| b |
| diff -r 8d676bbd1f2d -r 5149eb3a89c2 weblogolib/.__init__.py.kate-swp |
| b |
| Binary file weblogolib/.__init__.py.kate-swp has changed |
| b |
| diff -r 8d676bbd1f2d -r 5149eb3a89c2 weblogolib/__init__.py --- a/weblogolib/__init__.py Mon Jan 16 07:03:36 2012 -0500 +++ b/weblogolib/__init__.py Fri Jan 20 09:03:40 2012 -0500 |
| [ |
| @@ -132,6 +132,7 @@ altype="codonsT" offset=0 isreversed=False +show_warnings=False col=[] @@ -169,7 +170,7 @@ description = "Create sequence logos from biological sequence alignments." -__version__ = "1.0" +__version__ = "1.1" # These keywords are subsituted by subversion. # The date and revision will only tell the truth after a branch or tag, @@ -312,9 +313,9 @@ # Check that can get 80 characters in journal page @small # 40 chacaters in a journal column std_sizes = { - "small" : LogoSize( stack_width = 10, stack_height = 10*1*5), - "medium" : LogoSize( stack_width = 10*2, stack_height = 10*2*5), - "large" : LogoSize( stack_width = 10*3, stack_height = 10*3*5), + "small" : LogoSize( stack_width = 16.2, stack_height = 10*1*5), + "medium" : LogoSize( stack_width = 16.2*2, stack_height = 10*2*5), + "large" : LogoSize( stack_width = 16.2*3, stack_height = 10*3*5), } @@ -439,6 +440,7 @@ self.yaxis_scale = None self.show_xaxis = True + self.strict=False self.xaxis_label = "" self.xaxis_tic_interval =1 self.rotate_numbers = False @@ -798,7 +800,7 @@ "errorbar_width_fraction", "errorbar_gray", "small_fontsize", "fontsize", "title_fontsize", "number_fontsize", "text_font", - "logo_font", "title_font", + "logo_font", "title_font", "strict", "logo_label", "yaxis_scale", "end_type", "debug", "show_title", "show_xaxis", "show_xaxis_label", "show_yaxis", "show_yaxis_label", @@ -930,6 +932,8 @@ # Create and output logo template = resource_string( __name__, 'template.eps', __file__) + + logo = Template(template).substitute(subsitutions) print >>fout, logo @@ -1248,6 +1252,14 @@ if len(str(seqs[i][(counter):(counter+3)]))==3 and len(seqs[i][(counter):(counter+3)].strip("GATUC"))==0 : if(str(seqs[i][(counter):(counter+3)]) in alphabet): x[counter/3][ (alphabet.index(str(seqs[i][(counter):(counter+3)]))) ]+=1 + elif show_warnings: + if len(seqs[i][(counter):(counter+3)].strip("GATUC"))==1 or len(seqs[i][(counter):(counter+3)].strip("GATUC"))==2 : + print >>sys.stderr, 'Warning:Incomplete or non GATUC codon detected:', seqs[i][(counter):(counter+3)] + print >>sys.stderr, 'Position:',counter + print >>sys.stderr, 'Sequence:',i + print >>sys.stderr, 'This will be treated as ---' + + counter=counter+3 counts=asarray(x) else: @@ -1369,12 +1381,19 @@ if not line: break line = line.split() - priordict[line[0]]=line[1] - return priordict + + if(altype=="codonsT"): + priordict[line[0].upper().replace("U", "T")]=(float(line[1])/1000)*64 + else: + priordict[line[0].upper().replace("T", "U")]=(float(line[1])/1000)*64 + + return priordict def _build_logodata(options) : global offset offset=options.frame + global show_warnings + show_warnings = options.strict options.alphabet = None options.ignore_lower_case = False #options.default_color = Color.by_name("black") @@ -1384,7 +1403,7 @@ seqs = read_seq_data(options.fin, options.input_parser.read, alphabet=options.alphabet, - ignore_lower_case = options.ignore_lower_case) + ignore_lower_case = options.ignore_lower_case) if(options.priorfile!=None): if(altype=="CodonsT"): options.composition= str(read_priors(options.priorfile,codon_alphabetT)) @@ -1408,6 +1427,7 @@ "logo_title", "yaxis_label", "show_xaxis", + "strict", "show_yaxis", "xaxis_label", "show_ends", @@ -1644,7 +1664,13 @@ type="int", help="Upper bound of sequence to display", metavar="INDEX") - + + data_grp.add_option( "-G", "--strict", + dest="strict", + action="store", + type="boolean", + help="Issue warnings if partial codons are encountered. Default: %default",default = defaults.strict, + metavar="True/False") # ========================== FORMAT OPTIONS ========================== format_grp.add_option( "-s", "--size", |
| b |
| diff -r 8d676bbd1f2d -r 5149eb3a89c2 weblogolib/template.eps --- a/weblogolib/template.eps Mon Jan 16 07:03:36 2012 -0500 +++ b/weblogolib/template.eps Fri Jan 20 09:03:40 2012 -0500 |
| b |
| @@ -484,7 +484,7 @@ % 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 - 0.001 gt {}{pop 0.0} ifelse + 0.01 gt {}{pop 0.0} ifelse def char_height 0.0 gt { |