Tripped over a little problem that may be shell-related; I was hoping someone might have some insight, as I'm pretty naive about the Windows shell.
We have a make script that recursively runs egg2bam across all directories under a specific file path. We run the command by assembling a shell string ('egg2bam -o myfile.bam myfile.egg') and then using Python's 'os.popen' function to run the command.
When we do the above, it appears that ObjectType specifications we've defined in our Config.prc file aren't used---as if the file is never read. I'm not able to capture egg2bam's error pipe in this environment, so I can't be sure whether the file is getting loaded. In any case, the output bam lacks the substitutions that our egg-object-type-* config entries should have created; the ObjectType tags appear to simply vanish from the bam output. Running the exact same command line outside of the python script (i.e. outside the os.popen method) has the desired result; our ObjectType tags are substituted with the proper content as per the egg-object-type specifiers in our Config.prc file.
Has anyone experienced a similar problem, or could recreate the problem I described? How does egg2bam locate the Config.prc files? Is there perhaps another way to get python to execute a shell command that I could try?
Thank you for the help!