Delete profile_align.py

profile_align.py

-import os
-from multiprocessing import Pool, cpu_count
-import glob
-from subprocess import Popen, PIPE
-
-def get_aln_files(query, db):
-    aln_list = []
-    qlist = [x for x in os.listdir(query) if x.endswith(".fasta")];  dblist = os.listdir(db)
-    for qfile in qlist:
-        if qfile in dblist:
-            aln_list.extend([qfile])
-        else:
-            print qfile + ' is missing from db'
-    return aln_list
-
-def run_muscle(aln_file):
-    if not os.path.isfile(out+aln_file):
-        print aln_file
-        muscle_pars = ["muscle", "-profile", "-in1", db+aln_file, "-in2", query+aln_file, "-out", out+aln_file]
-        proc_muscle = Popen(muscle_pars, stdout=PIPE, stderr=PIPE)
-        stdout, stderr = proc_muscle.communicate()
-        print stderr
-    return
-
-def launch_muscle(aln_files, cores):
-    pool = Pool(cores, maxtasksperchild=32)
-    pool.map(run_muscle, aln_files)
-    pool.close()
-    pool.join()
-    return
-
-
-if __name__ == '__main__':
-    global query
-    global db
-    global out
-    out = '/mnt/scratch/traca001/data/test/'
-    query = '/mnt/scratch/traca001/data/genespades_preprocess_query/domains/'
-    db = '/mnt/scratch/traca001/data/genespades_preprocess_raw_2/domains/'
-    aln_list = get_aln_files(query, db)
-    print aln_list
-    launch_muscle(aln_list, cores=cpu_count())
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