I'm beginning to learn Python 2.7 and need to develop some applications for a lab project.
I want to run an external program and then use its output as input for another external call in the same script. The issue is that the script tries to call the second program even before the first one has finished working, so the output is not yet available to be used as its input.
How can I solve this problem?
Here is my code:
picker = Popen ([pick_open_reference_otus.py, -i, allseq_file, -r, refseq_file, -o, noName, -s, 0.1, -m, usearch61, -p, param_file ], shell = True)
picker_out = os.path.join(path, "otu_output/otu_table_mc2_w_tax.biom")
Thank you all!