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Laros authored
handling for incomplete and poorly annotated GenBank files. menu.html: - Template for all pages. Includes a menu and such. index.html: - The main page. base/: - Pictures, javascript, stylesheet, etc. interface.js: - Temporary script for gbupload.html. download.html: - Adjusted to work with the menu.html template. gbupload.html: - Adjusted to work with the menu.html template. check.html: - Extended the template to use more variables to increase flexibility. index.py: - Removed the capturing of the Mutalyzer output in the check() function, replaced it with retrieval of data from the Output object. - Added a new index() function (see index.html). - Implemented the upload() function (see gbupload.html), currently it can only retrieve genes and chromosome slices from the NCBI. Web.py: - Enabled the parsing of the menu.html template in the tal() function. handler.py: - Modified to work with the new tal() function of Web.py. Output.py: - getMessages() now returns a list of messages, instead of printing it to standard output. mail.txt: - Template message for finished batch jobs. Mutalyzer.py: - __bprint() now puts the visualisation of a protein in the Output object, instead of printing it to standard output. - Made a new protein printing function that can highlight the changes, it is not used yet. - Added a __cdsLen() function that is used to see if a variant leads to a frameshift or not. - Added extention of a protein in the protein description function. - Added some error handling for `?' as a position. - Added error messages for invalid genes and transcript variants in the input (suggesting possible options). - DNA / protein descriptions are now stored in the Output object. - Added a legend. GenRecord.py: - Added functions listLoci() and listGenes() for suggestions when invalid input is given. - Added a preprocessing step in the GenBank file parsing to deal with missing locus tags (not functional yet). - Added some error handling for incomplete transcripts. git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@52 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
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