I also use subprocess module. Actually, I think that is the only available module which you would and should prefer to use as commands module has been deprecated.
Regards, Palak Mathur http://palakmathur.wordpress.com http://vicharvahak.wordpress.com http://aatmiyata.wordpress.com http://palakmathur.blogspot.com On Tue, Aug 14, 2012 at 10:21 AM, Yoganand Anandaraju <yogan...@gmx.com>wrote: > I use subprocess.call to execute shell commands. Take a look at this > http://docs.python.org/library/subprocess.html > > ----- Original Message ----- > From: briji...@gmail.com > Sent: 08/14/12 08:51 AM > To: Bangalore Python Users Group - India > Subject: Re: [BangPypers] executing shell commands through python script > > try this. http://docs.python.org/library/commands.html Regards, Brijith > P On Tue, Aug 14, 2012 at 3:15 AM, Vikram K <kpguy1...@gmail.com> wrote: > > i am able to run the following command from the shell (i am working on > Mac > Snow Leopard): > > cgatools evidence2sam --beta --evidence-dnbs > > evidenceDnbs-chr11-GS000010026-ASM-T1.tsv.bz2 --reference build36.crr > > --output CGI_10026_CLL046_chr11_NUMA1_N.sam --extract-genomic-region > > chr11,71391559,71469221 --add-mate-sequence > > The command i give above > executes perfectly and i get the desired results. > Problem is that i need > to execute variations of this command around two > hundred times on the > shell. Can i embed this command in a python script (i > think one of the > functions in the os module might be able to do what i > want). Thanks. > > _______________________________________________ > BangPypers mailing list > > BangPypers@python.org > > http://mail.python.org/mailman/listinfo/bangpypers_______________________________________________ > BangPypers mailing list BangPypers@python.org > http://mail.python.org/mailman/listinfo/bangpypers > > > > Regards, > Yoganand > _______________________________________________ > BangPypers mailing list > BangPypers@python.org > http://mail.python.org/mailman/listinfo/bangpypers > _______________________________________________ BangPypers mailing list BangPypers@python.org http://mail.python.org/mailman/listinfo/bangpypers
