repseq_vdj.py, should-vdj-to-tap.py: VDJ_File()

New class VDJ_File() in repseq_vdj.py, responsible for loading and saving .vdj files

algo/tests/repseq_vdj.py

@@ -236,17 +236,59 @@ def should_results_from_vidjil(program, f_should, f_log):
 
 
 
+
+### VDJ File
+
+class VDJ_File():
+    '''
+    Handle .vdj files
+    These files contain (#, >) couples of V(D)J designations, such as in:
+    #TRDD2*01 1/AGG/1 TRDD3*01  TRD+
+    >TRDD2*01  TRDD3*01
+    '''
+
+    def __init__(self):
+        self.hr = []
+
+    def __iter__(self):
+        return self.hr.__iter__()
+
+    def __len__(self):
+        return len(self.hr)
+
+    def write(self, f):
+        for (header, result) in self.hr:
+            f.write("#%s\n" % header)
+            f.write(">%s\n" % result)
+            f.write("\n")
+
+    def parse_from_gen(self, gen):
+        self.hr = list(gen)
+
+    def parse_from_file(self, f):
+        should = ''
+        for l in f:
+
+            l = l.strip()
+            if not l:
+                continue
+
+            if l[0] == '#':
+                should = l[1:]
+
+            elif l[0] == '>':
+                self.hr += [ (should, l[1:]) ]
+
+
 ### Main
 
 if __name__ == '__main__':
 
+    vdj = VDJ_File()
+
     if 'mixcr' in sys.argv[1]:
-        gen = header_mixcr_results(sys.argv[1])
+        vdj.parse_from_gen(header_mixcr_results(sys.argv[1]))
     else:
-        gen = header_vquest_results(sys.argv[1], sys.argv[2])
+        vdj.parse_from_gen(header_vquest_results(sys.argv[1], sys.argv[2]))
 
-    # output .vdj data
-    for (header, result) in gen:
-        print "#%s" % header
-        print ">%s" % result
-        print
+    vdj.write(sys.stdout)

algo/tests/should-vdj-to-tap.py

@@ -65,28 +65,6 @@ global_stats_failed = defaultdict(int)
 global_stats_todo = defaultdict(int)
 
 
-def should_results_from_vdj(f_vdj):
-    '''
-    Parses a .vdj file
-    Yields (#, >) couples of V(D)J designations, such as in:
-    #TRDD2*01 1/AGG/1 TRDD3*01  TRD+
-    >TRDD2*01  TRDD3*01
-    '''
-
-    should = ''
-    for l in open(f_vdj):
-
-        l = l.strip()
-        if not l:
-            continue
-
-        if l[0] == '#':
-            should = l[1:]
-
-        elif l[0] == '>':
-            yield should, l[1:]
-
-
 def should_pattern_to_regex(p):
     '''
     Converts patterns such as the following ones into a Python regex.
@@ -306,7 +284,10 @@ if __name__ == '__main__':
         if '.vdj' in f_should:
             f_vdj = f_should
             f_tap = f_vdj + TAP_SUFFIX
-            write_should_results_to_tap(list(should_results_from_vdj(f_vdj)), f_tap)
+
+            vdj = repseq_vdj.VDJ_File()
+            vdj.parse_from_file(open(f_vdj))
+            write_should_results_to_tap(vdj, f_tap)
             continue
 
         should_to_tap_one_file(f_should)