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Feature #528

closed

collect metadata on the fly by passing a mutable object to generators

Added by Madeleine Ball about 13 years ago. Updated almost 13 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Target version:
-
Story points:
-

Description

I made a script (get_metadata.py) to collect metadata from the GFF file and other output files. However, this is time-consuming, we shouldn't read through files more than once.

Now that we have generator chaining for going through the GFF, one solution might be to make the metadata collection another generator. While this has the advantage of separating out this aspect of processing, there is some metadata which requires the output file rather than the GFF file -- in particular, finding out "percent called in coding regions" uses output from the script (gff_call_uncovered.py) that reports which coding regions are missing.

Instead I think metadata should stored in a mutable object optionally passed the generators -- if the generator has any metadata it wants to add, it adds it to the object. Probably a dict.


Related issues

Related to GET-Evidence - Feature #524: Report metadataResolvedMadeleine Ball02/17/2011Actions
Actions #1

Updated by Madeleine Ball about 13 years ago

  • Assigned To set to Madeleine Ball
Actions #2

Updated by Madeleine Ball almost 13 years ago

  • Status changed from New to Resolved
  • Resolution set to fixed

Added metadata storage to the progresstracker object in commit 0d88c715

Marking as resolved.

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