[Biopython-dev] [Biopython (old issues only) - Bug #3057] (Migrated) Incremental parsing in Bio.Emboss.PrimerSearch

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Issue #3057 has been updated by Peter Cock.

Description updated
Status changed from New to Migrated
URL set to https://github.com/biopython/biopython/issues/1727

Migrated to GitHub as https://github.com/biopython/biopython/issues/1727

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Bug #3057: Incremental parsing in Bio.Emboss.PrimerSearch
https://redmine.open-bio.org/issues/3057#change-15423

* Author: Peter Cock
* Status: Migrated
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: 1.54b
* URL: https://github.com/biopython/biopython/issues/1727
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The Bio.Emboss.PrimerSearch module has a single function "read" which loads and parses an entire output file from the EMBOSS tool primersearch into memory at once, returning what is essentially a dictionary keyed by primer name, with as values lists of amplimer information objects.

Even though this still seems to work with "large" output files for thousands of primer pairs, I think it would be useful to provide an iterator function "parse" returning the amplimers for each primer. The current "read" function could be retained for backward compatibility.

The parsing code itself could be extended to extract information like the forward and reverse primer sequences, where the hit (location and strand) and with how many mismatches. This information is currently all held in a long string.



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