apa.rnamotifs

#!/usr/bin/python3

import apa
import os
import sys
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('-comps_id', action="store", dest="comps_id", default=None)
parser.add_argument('-fdr', action="store_true", default=False)
args = parser.parse_args()

if args.comps_id!=None:
    comps_id = args.comps_id
    comps = apa.comps.Comps(comps_id)
    for site in ["proximal", "distal"]:
        for pt in ["same", "composite", "skipped", "all"]:
            rnamotifs_id = "%s_%s_%s" % (comps_id, site, pt)
            folder = os.path.join(apa.path.rnamotifs_folder, "comps", "%s_%s_%s" % (comps_id, site, pt))
            try:
                os.makedirs(folder)
            except:
                pass

            fname1 = os.path.join(apa.path.comps_folder, comps_id, "motifs", "tab", rnamotifs_id+".tab")
            fname2 = os.path.join(apa.path.rnamotifs_folder, "comps", rnamotifs_id, rnamotifs_id+".tab")
            os.system("perl -pe 's/r\n/s\n/g' %s > %s" % (fname1, fname2))
            fname_config = os.path.join(apa.path.rnamotifs_folder, "comps", rnamotifs_id, rnamotifs_id+".config")
            print fname_config
            f = open(fname_config, "wt")
            f.write("data_type=apa\n")
            f.write("hw=15\n")
            f.write("flanking=100\n")
            f.write("genome=%s\n" % comps.species)
            f.write('regions=[("r1", -80, -40), ("r2", 0, 40), ("r3", 40, 80)]\n')
            f.write("cores=4\n")
            if args.fdr:
                f.write("use_FDR=True\n")
            else:
                f.write("use_FDR=False\n")
            f.close()

            os.system("rnamotifs2 -comps %s" % rnamotifs_id)
            os.system("rnamotifs2.draw_apa -comps %s" % rnamotifs_id)