[Biopython-dev] [Bug 2419] New: SeqUtils __init__.py missing complement function (v1.43 and v1.44)

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2419

           Summary: SeqUtils __init__.py missing complement function (v1.43
                    and v1.44)
           Product: Biopython
           Version: 1.44
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: justin.t.riley at gmail.com


This issue exists in both 1.43 and 1.44.  You won't notice this bug on an
import of SeqUtils.  However, when you try to use the six_frame_translations
function like so:

from Bio import SeqUtils
SeqUtils.six_frame_translations('GTCA....AAT')

you get:

<type 'exceptions.NameError'>: global name 'complement' is not defined

at line 285 (for version 1.43 anyhow)

At first I searched all the Biopython modules for a "def complement" string and
found one in Seq but it was for the complement of an actual Seq object. 
Looking around the web I found:

def complement(seq):
    " returns the complementary sequence (NOT antiparallel) "
    return ''.join([IUPACData.ambiguous_dna_complement[x] for x in seq])

Pasting the above in Bio/SeqUtils/__init__.py solved the issue for me.  Thanks.

~jtriley


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