diff splitSHAPE.py @ 5:f4ad5dceb619 draft

planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 9a3dc91fa984be18fabc0d968360634d787c9589

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/splitSHAPE.py	Wed May 24 09:56:11 2017 -0400
@@ -0,0 +1,64 @@
+import os
+import re
+import sys
+
+shape_file = sys.argv[1]
+win_size = int(sys.argv[2])
+
+pattern = re.compile("^>.*$")
+toWrite = ""
+
+count_for_id = 1
+seq_counter = 0
+new_id = ""
+
+seq_id = []
+seq_string = []
+orig_id = []
+name_file = "FASTA/data.names"
+array_all_chunks = []
+with open(name_file, 'r') as f:
+    content = f.read()
+    lines = content.split('\n')[:-1]
+    for line in lines:
+        seq_id.append(int(line.split()[0]))
+        seq_string.append(line.split()[1])
+        orig_id_srt = line.split()[3]
+        orig_id_srt = orig_id_srt.rsplit('_',1)[0]
+        orig_id.append(orig_id_srt)
+
+
+react_dict = {}
+react_arr = []
+
+with open(shape_file, 'r') as shape:
+    content = shape.read()
+    lines = content.split('\n')
+    for line in lines:
+        if pattern.match(line):
+            line = line.replace('>','').strip()
+            react_arr=[]
+            react_dict[line] = react_arr
+            continue
+        else:
+            react_arr.append(line)
+
+toWrite = ""
+chunks = []
+for i in range(len(orig_id)):
+    if not orig_id[i] in react_dict:
+        raise RuntimeError('Error key {} not found'.format(orig_id))
+
+    react_val = react_dict[orig_id[i]]
+    toWrite += '>' + str(seq_id[i]) + " " + seq_string[i] + "\n"
+    chunks = re.findall(r'\d+', seq_string[i])
+
+    for j in react_val[int(chunks[1])-1:int(chunks[2])]:
+        id_s = int(j.split()[0])
+
+
+        id_s = id_s - int(chunks[1]) + 1
+        toWrite += str(id_s) + '\t' + j.split()[1] + "\n"
+
+with open("shape_data_split.react", 'w') as out:
+    out.write(toWrite)