[Biopython-dev] [Bug 1774] Bio.Clustalw: bug in computing the alignment.

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Apr 27 01:13:26 EDT 2005


mdehoon at ims.u-tokyo.ac.jp changed:

           What    |Removed                     |Added
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED

------- Additional Comments From mdehoon at ims.u-tokyo.ac.jp  2005-04-27 01:13 -------
Fixed in CVS, thanks.

The bug was caused by interpreting the return value of os.popen as the exit
status instead of the termination status. The exit status is the second byte of
the termination status, so we need to divide the result of os.popen by 256 to
get the exit status.
For example, if the C code of a program a.out contains
int main(void)
{  int status;
   return status;
then os.popen("a.out").close() returns status*256 instead of status. Same goes
for os.system. This is also true at the C-level, so this is not a Python bug.
Since we have calls to os.popen and os.system in various places in Biopython,
the same bug may appear elsewhere also.

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