added reorder

reorder.py

@@ -0,0 +1,66 @@
+#!/usr/bin/env python3
+
+"""
+    Usage:
+    ./reorder.py -r <FILE> -f <FILE>
+
+    Options:
+    -h, --help                     show options
+    -r, --reference <FILE>         reference sequence input
+    -f, --fasta <FILE>             fasta to reorder
+    --version                      print version
+"""
+import os
+import subprocess
+from Bio import SeqIO, SearchIO, Seq
+from docopt import docopt
+from depot.AladinFun import fichier_vide
+
+def reorder(reference,fasta):
+    FNULL = open(os.devnull, 'w')
+    blat_file = fasta + ".psl"
+    subprocess.call(["blat", fasta, reference, blat_file],stdout=FNULL,stderr=FNULL)
+    fichier_vide(blat_file)
+
+    qresult = SearchIO.read(blat_file, 'blat-psl')
+    hit_start = qresult[0][0].hit_range[0]
+    hit_end = qresult[0][0].hit_range[1]
+    hit_id = qresult[0].id
+    orientation = qresult[0][0].query_strand
+
+    if orientation > 0:
+        orientation = "+"
+    else:
+        orientation = "-"
+
+    assembly = {}
+    for record in SeqIO.parse(fasta, "fasta"):
+        elem = str(record.id).split(" ")
+        if orientation=="+":
+            assembly[elem[0]] = str(record.seq)
+        else:
+            assembly[elem[0]] = str(record.seq.reverse_complement())
+
+    circ_file = open(fasta+".reordered", 'w')
+    circ_file.write(">" + hit_id + "\n")
+    if orientation=="+":
+        pos = hit_start
+        circ_file.write(assembly[hit_id][pos:] + assembly[hit_id][:pos] + "\n")
+    else:
+        pos = len(assembly[hit_id])-hit_end
+        circ_file.write(assembly[hit_id][pos:] + assembly[hit_id][:pos] + "\n")
+    circ_file.close()
+
+    return(pos,orientation)
+
+def main():
+    args = docopt(__doc__, version='1.1')
+    reference = os.path.abspath(str(args['--reference']))
+    fasta = os.path.abspath(str(args['--fasta']))
+
+    reorder_position, orientation = reorder(reference,fasta)
+
+    print("Reordered fasta file at position " + str(reorder_position) + " with " + str(orientation) + " orientation.")
+
+if __name__ == "__main__":
+    main()