def run_cmsearch(fastas, threads, cm):
out = []<EOL>for fasta in fastas:<EOL><INDENT>cmsearch = '<STR_LIT>' % (fasta.name.rsplit('<STR_LIT:.>', <NUM_LIT:1>)[<NUM_LIT:0>])<EOL>if os.path.exists(cmsearch) is False:<EOL><INDENT>p = Popen('<STR_LIT>'% (threads, cmsearch, cm, fasta.name), shell = True)<EOL>p.communicate()<EOL><DEDENT>else:<EOL><INDENT>print('<STR_LIT>' % (cmsearch), file=sys.stderr)<EOL><DEDENT>out.append(open(cmsearch))<EOL><DEDENT>return out<EOL>
run cmsearch: comapre 23S sequences to ssu-align's CM