[Biopython-dev] [Bug 3057] New: Incremental parsing in Bio.Emboss.PrimerSearch

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3057

           Summary: Incremental parsing in Bio.Emboss.PrimerSearch
           Product: Biopython
           Version: 1.54b
          Platform: PC
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


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.


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.