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Script to generate dicty GPI file#110

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ypandit wants to merge 3 commits intodevelopfrom
feature/dicty-gpi
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Script to generate dicty GPI file#110
ypandit wants to merge 3 commits intodevelopfrom
feature/dicty-gpi

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@ypandit
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@ypandit ypandit commented Oct 22, 2013

  • Script to generate dicty-GPI
    • Caches gene names & synonyms using Hash
    • Caches Dicty-UniProt ID mapping using a Hash
  • Output file written as per GPI specs

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coveralls commented Oct 22, 2013

Coverage Status

Coverage decreased (-2.82%) to 37.4% when pulling 6390921 on feature/dicty-gpi into 1f47468 on develop.

@cybersiddhu
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cybersiddhu commented Oct 28, 2013

Needs cleanup.

  • Get rid of unnecessary private(underscore) variables. It's a class not designed with a public API, no need for polluting code with a barrage of underscore variables.
  • Loading the uniprot map, the code looks more complex than it should be.

@cybersiddhu
Removed underscore attributes
271486d 
Refactored building of gene products and synonyms
@cybersiddhu
Call the class method to properly register the extra relationship
17166dc 
accessor
Use BCS to get list of genes
Filter for pseudogene
Read a compressed gp2protein file for fetching uniprot ids
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@ypandit @coveralls @cybersiddhu