Testing

repeat-extractor.py

@@ -94,47 +94,50 @@ for line in lines:
     else:
         sequences[label] = [string.strip()]
 
-select = 'D13S317'
-unit_list = ['TATC']
-reference = sequences[select][0]
-sample = sequences[select][0]
-description, _, _ = describe_repeats(reference, sample, unit_list)
-print 'l.{}'.format(description)
-
-
-#for sequence in sequences:
-#    best = 0
-#    for string in sequences[sequence]:
-#        repeats = short_sequence_repeat_extractor(string, min_length)
-#        score = 0
-#        for repeat in repeats:
-#            if repeat.count + 1 >= min_count:
-#                score += (repeat.end - repeat.start) * (repeat.end - repeat.start) * (repeat.count + 1)
-#        if score > best:
-#            reference = string
-#            best = score
-
-#    repeats = short_sequence_repeat_extractor(reference, min_length)
-#    units = {}
-#    for repeat in repeats:
-#        if repeat.count + 1 >= min_count:
-#            units[reference[repeat.start:repeat.end]] = repeat.count + 1
-#    unit_list = []
-#    for unit in units:
-#        unit_list.append(unit)
-
-#    print sequence,
-#    if best > 0:
-#        print unit_list
-#    else:
-#        print 'no repeat unit identified'
-#    reference = sequences[sequence][0]
-#    for string in sequences[sequence]:
-#        if best > 0:
-#            description, _, _ = describe_repeats(reference, string, unit_list)
-#        else:
-#            description = describe_dna(reference, string)
-#        print 'l.{}'.format(description)
-#    print
+#select = 'D13S317'
+#unit_list = ['TATC']
+#reference = sequences[select][0]
+#sample = sequences[select][0]
+#description, _, _ = describe_repeats(reference, sample, unit_list)
+#print 'l.{}'.format(description)
+
+
+for sequence in sequences:
+    best = 0
+    for string in sequences[sequence]:
+        repeats = short_sequence_repeat_extractor(string, min_length)
+        score = 0
+        for repeat in repeats:
+            if repeat.count + 1 >= min_count:
+                score += (repeat.end - repeat.start) * (repeat.end - repeat.start) * (repeat.count + 1)
+        if score > best:
+            reference = string
+            best = score
+
+    repeats = short_sequence_repeat_extractor(reference, min_length)
+    units = {}
+    for repeat in repeats:
+        if repeat.count + 1 >= min_count:
+            units[reference[repeat.start:repeat.end]] = repeat.count + 1
+    unit_list = []
+    for unit in units:
+        unit_list.append(unit)
+
+    reference = sequences[sequence][0]
+    print sequence + ':',
+    print reference
+    if best > 0:
+        print 'repeat units:', unit_list
+    else:
+        print 'repeat units: []'
+    for string in sequences[sequence]:
+        rep_start = 1
+        rep_end = len(reference)
+        if best > 0:
+            description, rep_start, rep_end = describe_repeats(reference, string, unit_list)
+        else:
+            description = describe_dna(reference, string)
+        print '{}({}_{}):l.{}'.format(sequence, rep_start, rep_end, description)
+    print