1. 22 Jul, 2013 1 commit
  2. 10 Jul, 2013 1 commit
  3. 05 Jul, 2013 1 commit
  4. 25 Feb, 2013 1 commit
  5. 12 Feb, 2013 1 commit
  6. 29 Nov, 2012 1 commit
  7. 08 May, 2012 1 commit
  8. 12 Mar, 2012 1 commit
  9. 01 Feb, 2012 1 commit
  10. 04 Nov, 2011 1 commit
  11. 18 Aug, 2011 1 commit
  12. 21 Apr, 2011 2 commits
  13. 12 Apr, 2011 1 commit
  14. 11 Apr, 2011 1 commit
  15. 31 Mar, 2011 2 commits
  16. 23 Mar, 2011 3 commits
  17. 20 Dec, 2010 1 commit
  18. 11 Nov, 2010 1 commit
  19. 09 Sep, 2010 1 commit
    • Laros's avatar
      Fixed a bug that was triggered by incomplete exons in an EST reference sequence. · 31272838
      Laros authored
      - Increased the UpdateInterval window to three weeks (apparently 7 was too
        small since we sometimes miss an update).
      - Added mimetype guessing for all files in base/ (to make images cacheable and
        to reduce browser errors).
      - Fixed a bug that made the update program crash.
      - Added a function __checkExonList() that checks whether CDS start and CDS stop
        are in the list of gathered exons.
      - Added error handling for incomplete exon lists.
      - Updated the release date.
      - Fixed a syntax bug.
      - Fixed a syntax bug.
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@89 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
  20. 03 Sep, 2010 1 commit
    • Laros's avatar
      Mutalyzer.py: · 407fbe2b
      Laros authored
      - Made the ``multiple transcripts found'' message more descriptive.
      - Made the ``in frame stop codon'' check work for all organisms (and
      - Added mitochondrial DNA to the list of possible molecular types to be
        checked, it will be treated like genomic DNA.
      - Allowed genes without CDS list or mRNA list (only a CDS location) as a
        genomic description only if there are no other CDS's for that gene. 
      - Fixed a bug in the naming of the link method (it should also apply when mRNA
        is constructed from a CDS location only).
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@87 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
  21. 31 Aug, 2010 1 commit
  22. 04 Aug, 2010 2 commits
    • Gerben Stouten's avatar
      Minor Bug Fixes · 51318f49
      Gerben Stouten authored
      	Batch Jobs omit additional mutalyzer results when an error occures
      	Added the locus tag, transcriptProduct and proteinProduct
      	Removed transLongName & protLongName.
      	Substituted by transcriptProduct and proteinProduct
      	Empty lines in batch files are preserved
      	A better summary of errors is displayed
      	A threshold of 5% is set which omits erroreneous entries
      	Added the skip flag ~! for entries to be skipped at all
      	    Used for empty lines and lines that do not follow
      	    the formatting of either the new of old style
      	Added the option to set a flag when inserting an entry
      	Moved the error below the input form
      	Add threshold to config file
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@76 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
    • 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.
      - Added references for the TRM.
      - Documented a large part of the modules.
      - 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.
      - 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().
      - Separated the visualisation of a parse error from the error message. The 
        visualisation is now put in the output object as "parseError".
      - Added documentation.
      - 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.
      - Added file type information (for lrg and gb files).
      - Added sanity checks for the snpConvert() function.
      - Added documentation.
      - Added a new type "construction" to the linking methods, meaning that the
        mRNA is generated from the CDS.
      - Added an email variable for output to the website.
      - Added error information, to hide parts of the output.
      - Added file type information (see Retriever.py) to make download links more
      - Modified the syntax checker to work with the new parser output (see
      - Fixed a bug (selecting the human build) in the position converter.
      - Renamed download() to webservices().
      - Renamed ConversionChecker to PositionConverter.
      - Added.
      - Modified the template to work with the new restriction site format and the
        new parse error format.
      - Made lots of things conditional.
      - Added.
      - Added an example.
      - 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
  23. 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 
      - Added variables for splice site mutation detection.
      - Merged the restriction sites (added, deleted) in one object.
      - Changed the return type of getIndexedOutput() and getOutput() from None to
        an empty list for convenience.
      - Added variables for splice site mutation detection.
      - 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).
      - Added a snpConvert() function.
      - Added a check for uploaded records or slices that have no sequence in them
        (a complete contig for example).
      - Added variables to cope with chromosomal coordinates.
      - Added a toChromPos() function to convert a g. notation to a g. on a
      - 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.
      - Added a nomenclature version variable.
      - Added a urlEncode() function to generate valid links.
      - Made the getMimeType() function public.
      - 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.
      - Added guessing of mime types for downloadable files (it used to default to
      - 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
      - Modified to cope with the new functionality.
      - Restructured the layout.
      - New page for the SNP converter.
      - Modified to cope with the new functionality.
      - Modified to make some better tables and helper boxes.
      - Completely rewritten it.
      - 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
  24. 26 Jul, 2010 1 commit
    • Gerben Stouten's avatar
      Major fix for the batch runs · 808ea897
      Gerben Stouten authored
          * Updated the batch output generator
          * Make result file downloadable
          * Make webservice compatible with the new Mapper module
          * Updated functions to reflect new Mapper module
          * Added a redirect option to move get messages to the check form
          * Updated check to use the Session from redirect
          * implented __checkInt to catch user errors in upload
          * Added a progress option to get updates about batch progress
          * updated batch to show batch progress after submit
          * Added the AJAX request to get a batch progress counter
          * Started the linkify to change all Mutalyzer instances to clickable links
          * Added a hidden form to support the batch progress
          * Display Errors 
          * Added the getMessagesWithErrorCode
          * Made the seq a BioSequence for the restriction function
          * Added BatchFlags support to prevent jobs to hang at the same problem
          * Updated some returnvalues to reflect errors
          * Implemented the Flags to skip or alter other batch entries
          * Cleaned up the nameCheckerbatch significantly
          * Added a try/except clause around the namechecker to prevent batchhangs
          * Changed output fileextension to txt
          * Cleaned up Module
          * mainTranscript function updated to reflect webservice needs
          * Correct errors when retrieving fields from DB in _FieldsFromDb
          * Impemented entriesLeftForJob to get info about how a job is doing
          * Added updateBatchDb and skipBatchDb to skip/alter batch entries
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@71 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
  25. 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.
      - Added a rewrite rule to link to the bug tracker.
      - Updated the definition of the GBInfo table.
      - Added a new error (EPOS).
      - Made new images for the template (temporary).
      - Added a new class to make a form button look like a clickable link (used in
      - Added a new <td> class for right aligned text.
      - 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.
      - Added a conditional output section for uploaded sequences.
      - Changed the logos.
      - Added a link to the bug tracker.
      - Cleaned up the layout (indenting).
      - Added link to Gen2Phen.
      - 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
      - Changed the `visualisation' output list from a bare list to a list of 
      - Added verbose output to all raw variants.
      - Added productions for the EX and IVS position notations.
      - 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.
      - Added a version variable to the record class (not used yet).
      - Fixed a bug in matching transcripts and CDS by using a locus tag.
      - Added return values for downloadrecord() and uploadrecord(), so they can be
        used in index.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.
      - 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.
      - Testing.
      - 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.
      - 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.
      - 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 
      - 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
  26. 07 Jul, 2010 1 commit
    • Laros's avatar
      - Added the linkage of mRNA and CDS via their accession numbers. · 78dcb861
      Laros authored
      - Implemented the checking of shifting a deletion or insertion over a splice 
        site boundary in a transcript.
      - Added table definitions for the new Link table (used for the linkage of mRNA
        and CDS in the absence of locus tags).
      - Moved all functions to a GBparser class.
      - Added a transcriptToProtein() function that queries the database for a link
        between a transcript- and a protein accession number, if it is not found, the
        NCBI is queried to retrieve this link (and it is added to the local database).
      - Modified the createGBRecord() function to work with the new linkage function.
      - Added an email variable for the GBparser module (temporarily).
      - Added a function to the Gene class that creates a new locus tag.
      - Added a function to the Gene class that finds a link between a transcript and
        a CDS, based on the protein accession number.
      - Added the functions getProtAcc(), getmrnaAcc() and insertLink() for the
        linkage of transcript and CDS.
      - Changed the orientation input field to a select box.
      - Implemented the checking of shifting a deletion or insertion over a splice 
        site boundary in a transcript.
      - Fixed a bug in the description of a frameshift.
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@59 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
  27. 30 Jun, 2010 3 commits
    • Gerben Stouten's avatar
      Minor update CDS fix · a102d088
      Gerben Stouten authored
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/lrg@55 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
    • 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.
      - Template for all pages. Includes a menu and such.
      - The main page.
      - Pictures, javascript, stylesheet, etc.
      - Temporary script for gbupload.html.
      - Adjusted to work with the menu.html template.
      - Adjusted to work with the menu.html template.
      - Extended the template to use more variables to increase flexibility.
      - 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.
      - Enabled the parsing of the menu.html template in the tal() function.
      - Modified to work with the new tal() function of Web.py.
      - getMessages() now returns a list of messages, instead of printing it to 
        standard output.
      - Template message for finished batch jobs.
      - __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.
      - 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
    • Gerben Stouten's avatar
      Big update, LRG files now completely processed, annotation from updatable · d5a7ff70
      Gerben Stouten authored
      section included in record.
      Extracted code to create a GenRecord.Record from a GenBank file from
      GenRecord.py and included it in GBparser.py
      Updated the Retriever Module to facilitate two different retriever-types;
      LRGRetriever and GBRetriever.
      Updated the Db module with one method to update a LRG record in the database
      NOTE: Ensembl data is parsed but not yet included in the GenRecord.Record,
      because there is no clear usage for this. This behaviour can be changed in the
      LRGparser.py file
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/lrg@51 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
  28. 25 Jun, 2010 1 commit
  29. 23 Jun, 2010 1 commit
  30. 22 Jun, 2010 2 commits
  31. 14 Jun, 2010 1 commit
    • Laros's avatar
      Commit to do a merge with web_dev. This version is not suitable for · 48bb332d
      Laros authored
      distribution as it is under heavy development.
      Most modules will have minor changes because of a difference in set up of both
      the Db and Config module.
      - Added functionality to enable the cron restart of the Batch Checker.
      - Added the auto-generation of a .htaccess file.
      - Added permission settings.
      - Added configuration options for the Scheduler, File and GenRecord modules.
      - Described how to make the new ChrName tables for hg18 and hg19.
      - Added classifications to the messages.
      - Made a set up for the documentation.
        - This will be a technical document that describes the internals of the
          project. It is only meant for developers.
        - This is a description of the API, it is auto generated by the mkapidoc.sh
          script. Also only meant for developers.
      - Added a new roll function that will always find both boundaries.
      - Implemented a new protein naming scheme.
      - Fixed the trimming of a delins.
      - Rewrote the processing of a variant. 
        - Moved post processing of the GenBank record to the GenRecord module.
        - Moved the crossmapper instance to the GenBank module, to make one instance
          per transcript variant.
        - Moved the naming of a variant to the GenBank module, as is strongly
          interacts with the crossmapper instance.
      - Moved the constructCDS function to the GenRecord module.
      - Added functionality for the batch checker (retrieve results).
      - Added functionality for the genbank uploader (retrieve GenBank files).
      - Modified to work with the new Db module.
      - Modified to work with the new Db module.
      - Replaced the dictionary structure with a nested list structure to make
        iteration more convenient.
      - Added names to the Locus and Gene objects.
      - Added all information needed to do a crossmapping in the Locus object.
      - Wrote functions to find Loci and Genes.
      - Wrote a function that expands a description of a variant (coupled to a Locus).
      - Added documentation.
      - Added documentation.
      - Added documentation.
      - Added a function that checks whether a string is an e-mail address.
      - Implemented a batch scheduler that uses a MySQL database for queueing.
      - Implemented a CSV, XLS and ODS parser for use in the Scheduler module.
      - Added documentation.
      - Modified the complex object initialisation.
      - Made subclasses to configure the separate modules.
      - Added documentation.
      - Split the Db modules into different classes, according to functionality, they
        all inherit the query function from the Db base class.
      - Added chromosome accession number to name conversion functions and vice versa.
      - Added functionality for the batch checker.
      - Added documentation.
      - Added documentation.
      - Added fall back functionality when searching for a gene.
      - Added a batch submit interface.
      - The layout of the batch submit interface.
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@30 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
  32. 18 May, 2010 1 commit
    • Laros's avatar
      Altered the Output module in such a way that all messages are stored in a · 4a8a9986
      Laros authored
      list with priorities, and all output is stored in a dictionary. This dictionary
      can be read at a later time.
      The Retriever module is changed to accommodate for uploaded GenBank files and
      slices of a chromosome.
      A Scheduler was added for batch checking.
      - Added variables for the Retriever module:
        - maxDldSize, minDldSize ; Maximum and minimum sizes for slices and uploaded 
          GenBank files.
      - Added variables for the Output module:
        - loglevel, outputlevel ; Specify default verbosity levels for logging and 
      - Added variables for the Scheduler module:
        - processName ; Name of the running scheduler.
      - Added information on how to create the newly used tables GbInfo, BatchQueue
        and BatchJob.
      - Short description of the error codes used in the Output module.
      - Added a Complex class to test more complicated return types (see the web_dev
      - Modified the code to work with the new Output module.
      - Made a first upload page.
      - Modified the code to work with the new Output module.
      - Modified the code to work with the new Output module.
      - Modified the code to work with the new Output module.
      - Added documentation.
      - Modified the code to work with the new Output module.
      - New file, used for generating unique IDs.
      - Made a change to the definition of an UD accession number.
      - Modified the code to work with the new Output module.
      - Made a batch checker scheduler.
        - isDaemonRunning() ; See if we need to be started.
        - process() ; Start the batch checker.
        - addJob() ; Add jobs to a queue in the database.
      - Added a Message class to store all debug, info, warning, error and fatal
        - If a message is given that exceeds the configured log level, it will be
          logged immediately.
      - A function is added to the Output class to read all messages that exceed a 
        certain verbosity level.
      - A function is added to create a named list as an output node.
      - With the getOutput function the content of this list can be retrieved.
      - Several sub-classes were added for each configurable module.
      - Added documentation.
      - Added functionality that is used by the Retriever module.
      - Added functionality that is used by the Scheduler module.
      - Added functionality to be able to use custom GenBank files and chromosome
        - Information on these created files are stored in a database to be able to
          re-create them when the cache is cleaned.
        - The hash of each file is stored for error detection.
      - A wrapper that is called either from the addJob() function from the Scheduler
        module, or from cron. It dispatches a background process that processes the
        batch jobs.
      - Test template for uploading files (copied from Mutalyzer 1.0.4).
      - Some test with a complex return type.
      - Did some first tests with a METAL template.
      git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@26 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1