1. 13 Nov, 2015 1 commit
    • Vermaat's avatar
      wip · 43323c05
      Vermaat authored
      43323c05
  2. 02 Nov, 2015 1 commit
  3. 03 Jul, 2015 1 commit
  4. 26 May, 2015 1 commit
  5. 08 Dec, 2014 2 commits
  6. 24 Nov, 2014 2 commits
  7. 16 Jan, 2014 1 commit
    • Vermaat's avatar
      Port website from web.py to Flask · 0abce583
      Vermaat authored
      This includes changing a lot of routes and parameter names to be more
      consistent. We try to remain backwards compatible as much as possible
      by providing redirects from old routes and parameter names.
      0abce583
  8. 13 Dec, 2013 1 commit
  9. 21 Aug, 2012 1 commit
  10. 11 Jul, 2012 1 commit
  11. 18 Feb, 2012 1 commit
    • Laros's avatar
      Added the Variant Description Extractor as a web interface. · b8640a1f
      Laros authored
      describe.py:
      - Module that provides the Variant Description Extractor functions.
      
      __init__.py:
      - Added an automated copyright year update.
      
      website.py:
      - Added the Variant Description Extractor web interface.
      
      templates/descriptionExtract.html:
      -  Template page for the Variant Description Extractor.
      
      templates/snp.html:
      templates/menu.html:
      templates/converter.html:
      templates/index.html:
      templates/parse.html:
      - Cosmetic changes.
      
      Added a presentation.
      
      
      
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@479 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
      b8640a1f
  12. 29 Sep, 2011 1 commit
  13. 05 Apr, 2011 1 commit
  14. 09 Aug, 2010 1 commit
    • Laros's avatar
      First Beta release. · e0024265
      Laros authored
      Added help and about pages.
      
      Extended the TRM.
      
      Mutalyzer.py:
      - Added a __checkDNA() funtion for input checking.
      - Added a warning message for ``rolled'' insertions that are not duplications.
      - Added a warning for unsupported RNA descriptions.
      
      Web.py:
      - Added a release date variable.
      - Increased version numbers.
      
      index.py:
      - Added functions for the new pages (help.html and about.html)
      - Fixed a cosmetic bug that occurred when using html tags in the input.
      
      menu.html:
      - Made the top and bottom links compatible with Internet Explorer.
      - Added a link to the about page.
      - Added a link to the name generator page.
      - Removed some comment, altered some layout.
      
      index.html:
      - Moved some technical data to the about page.
      
      
      
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@78 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
      e0024265
  15. 04 Aug, 2010 1 commit
    • Laros's avatar
      Started on the TRM, therefore the separate files Db.txt and errorcodes.txt have · 0aa697dd
      Laros authored
      vanished. Fixed a large number of bugs.
      
      Db.txt, errorcodes.txt:
      - Renamed and converted to LaTeX.
      
      bibliography.bib:
      - Added references for the TRM.
      
      TechnicalReference.tex:
      - Documented a large part of the modules.
      
      Mutalyzer.py:
      - Added a __formatRange() function for better output of a range.
      - Added a __checkIntronPosition() function that checks the validity of an 
        intronic notation.
      - Fixed a bug that made a change in the first 9 nucleotides result in an
        unknown protein description.
      - Modified the error- and warning messages for large strings (see Mutator.py)
        and ranges.
      - Added a filter for indexing by protein isoform.
      
      Mutator.py:
      - Replaced the calculation of restriction sites using sets with code that does
        so using multisets. This allows the deletion of a site while an other site
        with the same name remains to be detected. Restriction sites are also
        reported in a more compact way.
      - Extracted the part of the visualisation where large strings are represented
        by their pre- and suffix and a number of omitted nucleotides. This is now
        available as a function visualiseLargeString().
      
      Parser.py:
      - Separated the visualisation of a parse error from the error message. The 
        visualisation is now put in the output object as "parseError".
      
      Output.py:
      - Added documentation.
      
      GBparser.py:
      - Moved the reverse-complement logic for the __findMismatch() function to the
        function itself.
      - Added an extra check for retrieving slicing information.
      - Added a filter for poorly annotated exons.
      - Added documentation.
      
      Retriever.py:
      - Added file type information (for lrg and gb files).
      - Added sanity checks for the snpConvert() function.
      - Added documentation.
      
      GenRecord.py:
      - Added a new type "construction" to the linking methods, meaning that the
        mRNA is generated from the CDS.
      
      Web.py:
      - Added an email variable for output to the website.
      
      index.py:
      - Added error information, to hide parts of the output.
      - Added file type information (see Retriever.py) to make download links more
        sensible.
      - Modified the syntax checker to work with the new parser output (see
        Parser.py).
      - Fixed a bug (selecting the human build) in the position converter.
      - Renamed download() to webservices().
      - Renamed ConversionChecker to PositionConverter.
      
      disclaimer.html:
      - Added.
      
      check.html:
      - Modified the template to work with the new restriction site format and the
        new parse error format.
      - Made lots of things conditional.
      
      skel.html:
      - Added.
      
      snp.html:
      - Added an example.
      
      menu.html:
      - Modified the layout, added some links, etc.
      
      Other templates:
      - Mainly edited the layout and indentation.
      
      
      
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@75 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
      0aa697dd
  16. 28 Jul, 2010 1 commit
    • Laros's avatar
      Rewrote the GBparser module to cope with multiple linking methods (to link · f299d5e6
      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
      f299d5e6
  17. 19 Jul, 2010 1 commit
    • Laros's avatar
      Implemented better visualisation of changes in the protein. Added IVS and EX · ca841562
      Laros authored
      notation. Implemented the detection of the addition or removal of restriction 
      sites. Added additional information about the transcript under scrutiny (if
      any), like the g. and c. positions of the exons, as well as the CDS start
      and stop.
      
      install.sh:
      - Added a rewrite rule to link to the bug tracker.
      
      Db.txt:
      - Updated the definition of the GBInfo table.
      
      errorcodes.txt:
      - Added a new error (EPOS).
      
      templates/base/images:
      - Made new images for the template (temporary).
      
      style.css:
      - Added a new class to make a form button look like a clickable link (used in
        check.html).
      - Added a new <td> class for right aligned text.
      
      check.html:
      - Made a lot of output conditional, depending on what Mutalyzer returns.
      - Made the submit forms conditional, depending on the method of retrieval:
        - GET ->  No forms.
        - POST -> Full output.
      - Added exon and CDS information.
      - Added restriction site information, coupled to the `raw variants'.
      - Added a download link for the reference sequence.
      - Made the affected transcripts clickable (post to Mutalyzer).
      - Added highlighting of changed amino acids for the protein changes.
      
      gbupload.html:
      - Added a conditional output section for uploaded sequences.
      
      menu.html:
      - Changed the logos.
      - Added a link to the bug tracker.
      
      index.html:
      - Cleaned up the layout (indenting).
      - Added link to Gen2Phen.
      
      Mutator.py:
      - Implemented the detection of the addition or removal of restriction sites.
        - Of each raw variant and its flanking sequences, two sets of restriction
          sites is constructed. One for the original subsequence and one for the
          mutated subsequence.
        - Additions and deletions can be detected by using the minus operator for
          sets.
      - Changed the `visualisation' output list from a bare list to a list of 
        triples.
      - Added verbose output to all raw variants.
      
      Parser.py:
      - Added productions for the EX and IVS position notations.
      
      Output.py:
      - Added a function that returns the data at the index in a list. Neither the
        list, nor the index need to be present, in which case None will be returned.
        This is convenient in index.py.
      
      GBparser.py:
      - Added a version variable to the record class (not used yet).
      - Fixed a bug in matching transcripts and CDS by using a locus tag.
      
      Retriever.py:
      - Added return values for downloadrecord() and uploadrecord(), so they can be
        used in index.py.
      
      GenRecord.py:
      - Added translate and transcribe variables to the Locus class, to be used to
        skip translation of non coding transcripts and to skip the processing of 
        incomplete transcripts as a whole.
      
      Web.py:
      - Revived the old tal parser to return a more basic html page (used when GET
        instead of POST is used in index.py). Mainly for LOVD.
      
      Scheduler.py:
      - Testing.
      
      Crossmap.py:
      - Updated comment.
      - Added:
        - getSpliceSite(), get the g. position of a splice site.
        - numberOfIntrons(), get the number of introns in a transcript.
        - numberOfExons(), get the number of exons in a transcript.
      
      index.py:
      - check():
        - Removed checks by using the getIndexedOutput() function.
        - Added a call to the `old' tal parser in case of a GET request.
        - Added more output (exon/CDS info, restriction sites, ...).
      - upload():
        - Implemented calls to the uploadrecord() and downloadrecord() functions of
          the Retriever module.
      
      Mutalyzer.py:
      - Implemented a new protein visualisation function that highlights the changes.
      - Used __toProtDescr() (and therefore the findInFrameDescription() and 
        findFrameShift() functions) to return the extent of the change, as well as a
        description of it. The extent is coded as a triple: (from, original end,
        variant end). This is used for the new visualisation.
      - Added a check for an inversion of length 1 (actually a substitution).
      - Added translation from EX and IVS positions (and ranges) to standard HGVS 
        positions.
      - Added a check for out of boundary positions (outside the reference sequence).
      - Added exon and CDS information to the output.
      - Made the translation of a CDS depend on the translate member variable of the
        Locus class.
      
      
      
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@66 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
      ca841562
  18. 30 Jun, 2010 1 commit
    • Laros's avatar
      Renewed the web interface. Worked on protein descriptions. Added more error · 2e170030
      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
      2e170030