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Laros authored
mRNA and CDS fields). Added a SNP converter. Implemented a first check for variants that hit splice sites. Added a chromosomal position for NC slices. Added a check for the use of intronic positions in a transcript reference sequence. mutalyzer.conf: - Added variables for splice site mutation detection. Mutator.py: - Merged the restriction sites (added, deleted) in one object. Output.py: - Changed the return type of getIndexedOutput() and getOutput() from None to an empty list for convenience. Config.py: - Added variables for splice site mutation detection. GBparser.py: - Completely rewrote this module. - Will now collect all CDS, mRNA and exon information. - Tries to match a CDS and mRNA based upon the range. - When this succeeds, try to match on protein, locus tag or product name. - If all fails and there is only one option left, link it. - Will remove genes that are not fully annotated (half outside the record for example). Retriever.py: - Added a snpConvert() function. - Added a check for uploaded records or slices that have no sequence in them (a complete contig for example). GenRecord.py: - Added variables to cope with chromosomal coordinates. - Added a toChromPos() function to convert a g. notation to a g. on a chromosome. - Added a addToChromDescription() function to generate a chromosomal description of a variant. - Modified some warnings concerning missing mRNA or missing CDS. - Added a checkIntron() function that gives a warning when a variant hits a splice site. Web.py: - Added a nomenclature version variable. - Added a urlEncode() function to generate valid links. File.py: - Made the getMimeType() function public. Mutalyzer.py: - Added a __intronicPosition() function that checks whether the user used an intronic position. - Added checks for illegal use of intronic positions. - Fixed a bug in the __toProtDescr() function. - Added more checks for the translation and transcription of transcripts. - Added a better CDS start site mutation detection. - Added a chromosomal description if available. - Added more information to the legend (product and linking method). - Merged the restriction sites (added, deleted) in one object. handler.py: - Added guessing of mime types for downloadable files (it used to default to text/plain). index.py: - Added a snp() function to interface with the snp() function of the Retriever. - Added a checkForward() function to accommodate for HTTP GET links. - Removed the `version' variable from all functions, it is now moved to the menu. check.html: - Modified to cope with the new functionality. gbupload.html: - Restructured the layout. snp.html: - New page for the SNP converter. menu.html: - Modified to cope with the new functionality. style.css: - Modified to make some better tables and helper boxes. index.html: - Completely rewritten it. parse.html: - Restructured the layout to make it uniform with the name checker. git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@73 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
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