[Biopython-dev] [Bug 2807] New: Clustalw return codes

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2807

           Summary: Clustalw return codes
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: cymon.cox at gmail.com


see bug 2804

More on clustalw return codes:

Note return codes are the same whether using subprocess.returncode or
(os.popen().close() \3)

clustalw1.81                  clustalw2.09
-----------------             ------------------
error: Bad command line option in the command: clustalw_bogus
-INFILE=Fasta/f002
127                           127

error: can't open sequence file: clustalw -INFILE=no_file_present
2                             255

error: wrong format of input file: clustalw -INFILE=Phylip/hennigian.phy
3                             255

error: only one sequence in input: clustalw -INFILE=Fasta/f001
4                             0

=========================================================

Clustalw.__init__ tries to catch return codes 1, 2, 3, and 4, others get caught
generically.

I dont think it is possible to generate a return code 1 using 1.81 because
interface doesnt allow ad hoc options to be added to the command line. Invalid
values of options are just ignore by clustalw and it aligns the data anyway (ie
return code 0).

Return codes 127 and 255 could be caught for newer versions and a more
informative error returned. But given that there are 9 other clustalw versions
between 1.81 (June 2003) and the latest 2.0.10 (Oct 2008 the latest) for which
I havent checked the return codes, it might be better to just return a generic
command line error if the return value is > 0.

In the case where only one sequence is present, newer versions return code 0,
but throws a ValueError when trying to parse the non-existent output file (see
comment in test_Clustalw_tools.py).

C.


-- 
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.