Hi all, I have a strange question. a program on shell looks as follows: $cat test.fa |fasta34 -q @ s where test.fa contains a protein sequence (alphabets); s is the database to be searched and @ +indicates that the input is from stdin (ie., 'cat test.fa') now instead of 'cat test.fa' i take that input into a varaible and want to feed it to the +program. I have a sequence string in a variable named x, and use subprocess module to wrap this: ######code start ###### import subprocess as sp x = 'GSQIPSHYWKKNLWYYSHEIDGGCHNMW' p0 = sp.Popen(["echo",x], stdout=sp.PIPE) p1 = sp.Popen(["fasta34","-q","@",s],stdin=p0.stdout, stdout=sp.PIPE) output = p1.communicate()[0] print output ########code end#####
Output for this code doesnt give me the result as the program senses the input as empty let me know where i am wrong. The idea is to pipe-input the string to the program as a variable as mentioned above. regards, KM -- http://mail.python.org/mailman/listinfo/python-list
