git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@154 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@152 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@140 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Db.py:
- Fixed the UCSC update bug by looking at the time, instead of the modDate.

Web.py:
- Updated the release date.

trunk:
- Put the directory var/ on ignore.

TechnicalReference:
- Put TechnicalReference.pdf on ignore.

API:
- Put api.pdf on ignore.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@136 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@134 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

andfixed a bug in the GenBank parser.

version 2.0 bugs.txt, beta-feedback.pdf, suggestions.txt, beta-feedback.txt:
- Suggestions, bugs, todo lists, ...

mutalyzer.sql:
- Definitions of the mutalyzer database (to be merged with documentation).

Install.txt:
- Added the definition of the map table.

batch.html:
- Modified the help text to reflect the internal functionality.

Mutalyzer.py:
- Added the function __overSplice() that checks whether a splice site is 
  destroyed.
- Added a check for splice site destruction by calling aforementioned function.

webservice.py:
- Removed a typo (getGeneAndTranscipt() -> getGeneAndTranscript()).

Mutator.py:
- Reinstated the insertion of sequences on splice junctions to be added to the
  exon instead of the intron.
- Fixed a bug in the shiftpos() function.

GBparser.py:
- Fixed a bug that was triggered if the input is a minimally annotated one-exon
  gene.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@133 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/soaplib-branch@121 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/soaplib-branch@120 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Fix for None value returned by getIndexedOutput. Added webservice name. Fix webservice for use with Apache/mod_wsgi.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/soaplib-branch@119 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/soaplib-branch@118 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/soaplib-branch@117 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/soaplib-branch@116 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- Implemented SOAP interface using soaplib.
- The SOAP interface is now a standalone WSGI server.
- Added some tests for the SOAP service.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/soaplib-branch@115 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/soaplib-branch@114 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@112 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

bnf.tex, Parser.py:
- Updated documentaion of the BNF.

webservice.py:
- Added logging to the getGeneAndTranscipt() function.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@111 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@110 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@109 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

and added a couple of functions to the webservice.

doc:
- Added all presentations given on Mutalyzer.

doc/TechnicalReference/bnf.tex:
- Updated the documentation of the BNF.

Mutalyzer.py:
- Added a check for a valid start position in the __rv() function. If it is not
  set, the parser has accepted the variant description, but did not do anything
  more (unimplemented variant types for example). An ``unknown error'' is
  returned for now.
- Added the following to the output object in the __ppp() function, needed by
  the runMutalyzer() function of the webservice:
  - Original genomic reference sequence.
  - Mutated genomic reference sequence.
  - Original RNA sequence.
  - Mutated RNA sequence.
  - Original CDS sequence.
  - Mutated CDS sequence.
  - Original Protein sequence.
  - Mutated Protein sequence.
  - Alternative Protein sequence.

webservice.py:
- Added a function getTranscriptsByGeneName() that returns a list of
  transcripts, given a gene name.
- Fixed the getTranscriptsRange() function (see Mapper.py).
- Added the sequences described above in the Mutalyzer.py section to the output
  of the runMutalyzer() function.
- Added the summary of the output messages to the return object of the
  runMutalyzer() function.
- Added a getGeneAndTranscipt() function, that given a genomic reference
  sequence and a transcript accession number (NM_...) returns the gene name and
  transcript variant. 

Serializers.py:
- Modified the MutalyzerOutput class to contain the values described in the
  Mutalyzer.py and webservice.py section.

Scheduler.py:
- Modified a call to chrom2c(), (see Mapper.py).

Mapper.py:
- Added an extra check on the start location (also see Mutalyzer.py, first
  point).
- Modified the chrom2c() function to use an additional argument to control the
  return type. It can now either return a list or a dictionary.

Db.py:
- Added a function get_TranscriptsByGeneName(), for the
  getTranscriptsByGeneName() function of the webservice.

VarInfo.py:
- Added (commented out) debug code.

index.py:
- Modified a call to chrom2c(), (see Mapper.py).

sp.py:
- Added examples for (some of) the new functions of the webservice.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@108 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@105 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

EST. Made the runMutalyzer() function in the webservices more robust and added
some better error messages in the Retriever module.

Mutalyzer.py:
- A deletion in the first 3 nucleotides on an EST resulted in a crash, this is
  fixed.
- A delins with a deletion and an insertion with either a common prefix or
  suffix was handled incorrectly.

webservice.py:
- Made the retrieval of information in the runMutalyzer() function more robust
  by using the getIndexedOutput() function of the Output object.

Retriever.py:
- Added a more sensible error when a record could not be retrieved.

menu.html:
- Fixed some capitalisation for more consistency in the web pages.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@104 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- Fixed a bug that was triggered when a wrong range was given, now an error is
  returned.

Web.py:
- Modified the release date.

menu.html:
- Updated the link to Mutalyzer 1.0.4.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@103 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- Added misc_RNA, ncRNA, rRNA, tRNA and tmRNA as valid RNA fields.

GenRecord.py:
- Enabled the transcription of non-coding RNA.

Web.py:
- Increased the version number and release date.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@102 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

fixed a bug that was triggered when a range is used in combination with a
genomic notation.

webservice.py:
- Added a function runMutalyzer(), full programmatic access to Mutalyzer (to 
  be expanded).

Serializers.py:
- Added the class MutalyzerOutput() which will contain any data needed by the
  webservice. For now it only contains the original and mutated DNA sequence.

sp.py:
- Added the new runMutalyzer() function to the examples.

GenRecord.py:
- Activated the transcription of non-coding RNA.

GBparser.py:
- Added the gathering of non-coding RNA data from an NR reference sequence.

Mutalyzer.py:
- Fixed a bug that was triggered when a range is used in combination with a 
  genomic notation.
- Added the full original and mutated string to the output object for use in
  webservices.

Parser.py:
- Corrected some comment.

bnf.tex:
- Synchronised the BNF with the functionality of the parser.

help.html:
- Corrected some text.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@99 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

is in fact a duplication. The duplicated region was reported incorrectly.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@96 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

reference to it. This script was not executed because of this.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@92 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@91 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Made some minor changes in the html templates.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@90 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

mutalyzer.conf:
- Increased the UpdateInterval window to three weeks (apparently 7 was too
  small since we sometimes miss an update).

handler.py:
- Added mimetype guessing for all files in base/ (to make images cacheable and
  to reduce browser errors).

UCSC_update.py:
- Fixed a bug that made the update program crash.

GenRecord.py:
- 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.

Web.py:
- Updated the release date.

menu.html:
- Fixed a syntax bug.

style.css:
- Fixed a syntax bug.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@89 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@88 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- Made the ``multiple transcripts found'' message more descriptive.
- Made the ``in frame stop codon'' check work for all organisms (and
  organelles).

GBparser.py:
- 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. 

GenRecord.py:
- 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

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@86 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Lots of comments





git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@85 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

offset in the intron notation.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@84 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@83 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- The `*' (after STOP codon) was not interpreted in one case.

Fixed a bug that was introduced while adding the intron (and upstream and
downstream) notation check:
- Checks were not working for transcripts on the minus strand.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@82 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@81 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Mutator.py:
- In the newSplice() function, The call to shiftpos() is changed back to the
  original one. This version (shiftpos(i + 1) - 1) was done to make an
  insertion at the end of an exon possible. So this functionality is not
  available right now.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@80 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Wrote documentation:
- Removed the bibliography database and replaced it with a (generated) bbl
  file.
- Wrote a number of new sections in the TRM.
- Modified the Makefile for the new bibliography method.

Mutalyzer.py:
- Added documentation.
- Reinstated the ``alternative protein'' (alternative start codon).
- Added the molType to the output object, this is needed in the check.html
  template.

Scheduler.py:
- Fixed a bug that made any position conversion batch job crash.

File.py:
- Fixed a bug that made every batch job with no errors in the input crash.

index.py:
- Added a variable genomicDNA to the arguments in the check() function.
- Fixed a bug in the syntaxCheck() function, that made the syntax checker
  crash.

check.html:
- Added a ``clear field'' button.
- Added different headers for genomic DNA and mRNA.
- Modified the ``alternative protein'' visualisation.

snp.html:
- Added a ``clear field'' button.

menu.html:
- Fixed a bug in the background image.
- Removed the link to HGVS_nomenclature_extension_proposal.pdf and made it an
  external link.
- Added a link to Mutalyzer 1.0.4.

menu.js:
- Added a clearForm() function that clears one element in a form.

converter.html:
- Added a ``clear field'' button.

parse.html:
- Added a ``clear field'' button.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@79 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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