--- a/armdb_mirbase.py	Sun May 08 09:25:08 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,137 +0,0 @@
-import subprocess
-import argparse
-import time
-import urllib.request
-from multiprocessing import Process, Queue
-import itertools
-
-#---------------------------------Arguments------------------------------------------
-
-subprocess.call(['mkdir', 'out'])
-parser = argparse.ArgumentParser()
-
-parser.add_argument("-pos", "--positions", help="number of additional nucleotides", action="store")
-parser.add_argument("-tool_dir", "--tool_directory", help="tool directory path", action="store")
-parser.add_argument("-gen", "--genome", help="genome version", action="store")
-parser.add_argument("-gff3", "--gff", help="gff file",action="store")
-args = parser.parse_args()
-
-#-----------------------Download and read of the gff3 file---------------------------------
-
-def read_url(q):
-
-    url = 'https://www.mirbase.org/ftp/CURRENT/genomes/'+args.gff
-    data = urllib.request.urlopen(url).read()
-    file_mirna = data.decode('utf-8')
-    file_mirna = file_mirna.split("\n")
-    q.put(file_mirna)
-
-
-#-----------------------Export of the original gff3 file---------------------------------
-
-def write_gff(file_mirna):
-    f = open('original_mirnas.bed', "w")
-
-    for i in range(len(file_mirna)):
-        f.write(file_mirna[i] + "\n")
-
-#------------------------Process and export of the file with mature mirnas-------------------------------
-
-def new_gff(file_mirna):
-
-    mirna = []   		     # new list with shifted mirnas
-    positions =int(args.positions)   # positions shifted
-    print(str(positions)+" positions shifted")
-    names=[]
-
-    for i in range(len(file_mirna)):
-
-        # Remove lines which conatain the word "primary"
-        if "primary" not in file_mirna[i]:
-            mirna.append(file_mirna[i])
-
-            # Check if the line starts with "chr"
-            if "chr" in file_mirna[i]:
-                a=file_mirna[i].split("\t")[0]
-                b=file_mirna[i].split("\t")[6]
-                c=file_mirna[i].split("=")[3].split(";")[0]
-                names.append([a,b,c])
-
-    names.sort()
-    sublists=[]
-
-    [sublists.append([item] * names.count(item)) for item in names if names.count(item)>=2]
-    sublists.sort()
-    sublists=list(sublists for sublists, _ in itertools.groupby(sublists))
-    unique_names=[[x[0][0],x[0][2]] for x in sublists]
-
-    for x in unique_names:
-        flag = 0
-        for i in range(len(mirna)):
-
-              if "chr" in mirna[i] and mirna[i].split("=")[3].split(";")[0]==x[1] and x[0]==mirna[i].split("\t")[0]:
-                 flag+=1
-                 ktr=mirna[i].split(";")[0]+";"+mirna[i].split(";")[1]+";"+mirna[i].split(";")[2]+"-{"+str(flag)+"}"+";"+mirna[i].split(";")[3]
-                 mirna[i]=ktr
-
-
-    f = open('shifted_mirnas.bed', "w")
-
-    for i in range(len(mirna)):
-
-        if "chr" in mirna[i]:
-
-            # change the name of current mirna
-            mirna_name_1 = mirna[i].split("=")[3]
-            mirna_name_2 = mirna[i].split("=")[4]
-            mirna_name_1 = mirna_name_1.split(";")[0]+"_"+mirna_name_2+"_"+mirna[i].split("\t")[0]
-            mirna[i] = mirna[i].replace("miRNA", mirna_name_1)
-
-            # Shift the position of mirna
-            start = mirna[i].split("\t")[3]
-            end = mirna[i].split("\t")[4]
-            shift_start = int(start)-positions	# shift the interval to the left
-            shift_end = int(end)+positions	# shift the interval to the right
-
-            # Replace the previous intervals with the new
-            mirna[i] = mirna[i].replace(start, str(shift_start))
-            mirna[i] = mirna[i].replace(end, str(shift_end))
-
-            f.write(mirna[i] + "\n")
-
-    f.close()
-
-
-#------------------------Extract the sequences of the Custom Arms with getfasta tool-------------------------------
-
-def bedtool(genome):
-    subprocess.call(["bedtools", "getfasta", "-fi", "/cvmfs/data.galaxyproject.org/byhand/"+genome+"/sam_index/"+genome+".fa", "-bed", "shifted_mirnas.bed", "-fo", "new_ref.fa", "-name", "-s"])
-#===================================================================================================================================
-
-
-if __name__=='__main__':
-
-    starttime = time.time()
-    q = Queue()
-
-    # Read the original gff3 file
-    p1 = Process(target=read_url(q))
-    p1.start()
-    p1.join()
-    file_mirna=q.get()
-
-    # Export the original gff3 file
-    p2 = [Process(target=write_gff(file_mirna))]
-
-    # Create the new gff3 file
-    p2.extend([Process(target=new_gff(file_mirna))])
-    [x.start() for x in p2]
-    [x.join() for x in p2]
-
-    # Extract the sequences of the Custom Arms
-    p3 = Process(target=bedtool(args.genome))
-    p3.start()
-    p3.join()
-
-    print('Runtime: {} seconds'.format(round(time.time() - starttime,2)))
-