andrewhill157/leiden

Issues

• _LOVD3GeneData occasionally fails when attempting to extract text from a field that begins with HTML

  #45 opened 8 years ago by falquaddoomi
  0

• _LOVD3Database doesn't acquire full list of genes

  #44 opened 8 years ago by falquaddoomi
  0

• Update validation script command line interface

  #43 opened 11 years ago by andrewhill157
  0

• Splice/Intron/UTR Variant Validation

  #42 opened 11 years ago by andrewhill157
  0

• Loosen Broad Cluster Dependencies

  #40 opened 11 years ago by andrewhill157
  1

• Look into changing to VEP Remapping

  #41 opened 11 years ago by andrewhill157
  2

• Loosen Broad Cluster Dependencies

  #39 opened 11 years ago by andrewhill157
  0

• Need to finish proper notation of non-SNP variants to a VCF like format.

  #3 opened 11 years ago by andrewhill157
  1

• Examine flags in processed annotation data to determine causes.

  #7 opened 11 years ago by andrewhill157
  1

• Add unit tests

  #20 opened 11 years ago by andrewhill157
  2

• Introduce better error handling for link extraction

  #28 opened 11 years ago by andrewhill157
  0

• Modify initial filetering of extracted Leiden Data

  #23 opened 11 years ago by andrewhill157
  1

• Integrate Mutalyzer WebServices to automate remapping

  #32 opened 11 years ago by andrewhill157
  10

• Handle empty entries on database more gracefully

  #33 opened 11 years ago by andrewhill157
  2

• Some LOVD3 genes list multiple reference transcripts

  #34 opened 11 years ago by andrewhill157
  2

• Fix bug: genes with over 1000 entries are cut off at 1000 with current script

  #27 opened 11 years ago by andrewhill157
  2

• Ensure header label extraction is robust.

  #31 opened 11 years ago by andrewhill157
  0

• Write code to generate pseudo-VCF output files

  #37 opened 11 years ago by andrewhill157
  0

• Test Issue

  #38 opened 11 years ago by andrewhill157
  0

• Look into REST API service for LOVD

  #36 opened 11 years ago by andrewhill157
  0

• Ensure data sent to Monkol has consistent header ordering

  #30 opened 11 years ago by andrewhill157
  2

• Split remapped entries into CHROM #, COORDINATE, REF, ALT in output file

  #35 opened 11 years ago by andrewhill157
  1

• Fix line break error in data extraction script

  #13 opened 11 years ago by andrewhill157
  0

• Finalize which columns of data to include in open refine output and their format.

  #2 opened 11 years ago by andrewhill157
  1

• Discuss Indels with Monkol

  #21 opened 11 years ago by andrewhill157
  0

• Discuss validation more closely with Monkol.

  #22 opened 11 years ago by andrewhill157
  0

• Discuss DMD variants with monkol

  #26 opened 11 years ago by andrewhill157
  0

• Add Full LOVD3 Support

  #29 opened 11 years ago by andrewhill157
  2

• Make function that can automatically rename mutalyzer downloads

  #12 opened 11 years ago by andrewhill157
  2

• Clean up file delimiter and file naming inconsistencies.

  #25 opened 11 years ago by andrewhill157
  0

• Look into extracting data from entire Leiden Database

  #24 opened 11 years ago by andrewhill157
  4

• Update documentation

  #17 opened 11 years ago by andrewhill157
  1

• Update all command line arguments to argsparse.

  #16 opened 11 years ago by andrewhill157
  2

• Examine failures in variant extraction, remapping, and combination with original data.

  #14 opened 11 years ago by andrewhill157
  0

• Start using pycharms IDE

  #19 opened 11 years ago by andrewhill157
  0

• Migrate code to Python 3.3

  #18 opened 11 years ago by andrewhill157
  0

• Look into better command line interfaces

  #15 opened 11 years ago by andrewhill157
  1

• Add refseq id automatic extraction.

  #1 opened 11 years ago by andrewhill157
  0

• Make command line scripts have process all and process lists of specific inputs functionality.

  #11 opened 11 years ago by andrewhill157
  0

• Process additional genes from Leiden and send to Monkol.

  #8 opened 11 years ago by andrewhill157
  1

• Make a script to combine mutalyzer output and original input files.

  #9 opened 11 years ago by andrewhill157
  0

• Investigate how hard it would be to port open refine recipe to python.

  #10 opened 11 years ago by andrewhill157
  0

• Add script to flag mutations in Monkol's annotation data.

  #6 opened 11 years ago by andrewhill157
  1

• Need to validate mappings from mutalyzer output.

  #4 opened 11 years ago by andrewhill157
  1

• Fix body position when header changes for smaller screen sizes.

  #5 opened 11 years ago by andrewhill157
  1