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Clinvar import #333

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Clinvar import #333

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@mkroon1 mkroon1 commented Jan 18, 2018

Script to import variants from Clinvar's (gzipped) files.

  • Default source files point to Clinvar's FTP server.
  • Form let's one select user that serves as the owner of the newly imported variants.
  • Previously existing variant descriptions (from another submitter) are left untouched, the "clinvar variant" is imported as a separate entry.
  • Import consists of 3 phases:
    1. Import genomic variant descriptions
    2. Import descriptions on transcripts
    3. Import variant effects.
  • Script allows one to download list of unparsable variant descriptions after import.
  • Successive imports will not duplicate variants, instead variants are only updated when their description is changed.

mkroon1 added 13 commits November 30, 2017 16:52
@mkroon1
Initial version of script to import clinvar data. (WIP)
846d6c7
@mkroon1
Added unit test for reading GZipped Clinvar HGVS file.
25d59b9
@mkroon1
Cleanup Clinvar import and add documentation to code.
7fe8cf9 
* Removed code for debugging purposes.
* Prettify statistics output.
* Added adjustable parameter for user ID under which variants are
  imported.
* Improved code comments.
@mkroon1
Fix issue with redundant HTML doctype.
6c8c9ef
@mkroon1
More user friendly selection of user ID in clinvar import.
77bc456
@mkroon1
Save unparsable clinvar variants during import.
fbd7726 
* After import, unparsable variants from Clinvar are stored in a file in
  the temp directory. The file is overwritten with every run of the
  script.
* The file can be downloaded for users with manager clearance.
@mkroon1
Fix rowlink viewlist ID in lovd2 conversion script.
cb42953
@mkroon1
Provide transcript to lovd_getVariantInfo() during Clinvar import.
2531b65
@mkroon1
Fix user viewlist in clinvar import form.
87e2bc5
@mkroon1
Set variant effect during clinvar import.
533abb7 
* Loop over variant summary file.
* Link `clinical significance` field to LOVD's `var_effect`.
* Update objects that have a different value for effectid than in the
  database.
@mkroon1
Fix test Clinvar file for new default constructor values.
c745092
@mkroon1
Store variant effect values for clinvar records.
5577d94 
* Translate Clinvar's "clinical significance" to LOVD's
  "variant_effect", taking the most severe value.
* Store original "clinical significance" value in
  "VariantOnTranscript/Classification".
* Modify Clinvar file class to handle arbitrary compression factors.
@mkroon1
Fix default locations Clinvar source files.
fbfddf2
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