Renamed SOAP webservice from MutalyzerService to Mutalyzer.
Updated copyright years in HTML template.
Added test checking availability of WSDL file.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@160 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@159 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Set web.py debugging mode. Refactored rendering of static pages into one handler class (Static). In the generated webservice documentation, get the WSDL directly from the webservice module instead of through a HTTP request. Also fixed this generated webservice documentation to have a text/html content type.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@158 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@157 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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