Add files via upload

slide_gc.py

@@ -0,0 +1,42 @@
+import argparse
+import sys
+def parseFasta(filename): #seq_api
+    fas = {}
+    idlis = []
+    id = None
+    with open(filename, 'r') as fh:
+        for line in fh:
+            if line[0] == '>':
+                header = line[0:].rstrip()
+                id = header.split()[0]
+                idlis.append(id)
+                fas[id] = []
+            else:
+                fas[id].append(line.rstrip())
+        for id, seq in fas.items():
+            fas[id] = ''.join(seq)
+    return fas
+
+def gc_slide():
+    parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    parser.add_argument("-f", "--fasta", action="store", dest="fasta_name", required=True)
+    parser.add_argument("-s", "--step", action="store", type = int,dest="step", default =20000)
+    parser.add_argument("-w", "--window", dest="window_size",type = int,default =100000)
+    args = parser.parse_args()
+    fasta_name = args.fasta_name
+    step = args.step
+    window_size = args.window_size
+    if step >window_size:
+        print("ERROR! step can't be bigger than window.")
+        sys.exit()
+    genome_fa = parseFasta(fasta_name)
+    print("chr start end gc_count")
+    for CHR,SEQ in genome_fa.items():
+        i=0
+        while i<len(SEQ):
+            x = SEQ[i:i+window_size]
+            if len(SEQ)-i>=window_size:
+                print(CHR.strip('>'),i+1,i+window_size,(x.upper().count('G')+x.upper().count('C'))/len(x))
+            i=i+step
+if __name__ == "__main__":
+    gc_slide()