Removed deletions from repeat structure description

extractor/describe.py

@@ -391,13 +391,13 @@ def describe_repeats(reference, sample, units):
                 i += 1
             if i < variant.sample_end:
                 split = extractor.Variant()
-                split.reference_start = variant.reference_start
-                split.reference_end = variant.reference_end
+                split.reference_start = variant.reference_start + reference_start
+                split.reference_end = variant.reference_end + reference_start
                 split.sample_start = start
                 split.sample_end = i
                 split.type = variant.type
-                split.transposition_start = variant.transposition_start
-                split.transposition_end = variant.transposition_end
+                split.transposition_start = variant.transposition_start + reference_start
+                split.transposition_end = variant.transposition_end + reference_start
                 replaced.append(split)
                 while i < variant.sample_end and masked_alt[i + sample_start] == MASK:
                     i += 1
@@ -405,13 +405,13 @@ def describe_repeats(reference, sample, units):
 
         if len(replaced) > 0:
             split = extractor.Variant()
-            split.reference_start = variant.reference_start
-            split.reference_end = variant.reference_end
+            split.reference_start = variant.reference_start + reference_start
+            split.reference_end = variant.reference_end + reference_start
             split.sample_start = start
             split.sample_end = variant.sample_end
             split.type = variant.type
-            split.transposition_start = variant.transposition_start
-            split.transposition_end = variant.transposition_end
+            split.transposition_start = variant.transposition_start + reference_start
+            split.transposition_end = variant.transposition_end + reference_start
             replaced.append(split)
             variant_list += replaced
         else:
@@ -449,7 +449,7 @@ def describe_repeats(reference, sample, units):
         elif variant.type & extractor.REVERSE_COMPLEMENT:
             seq_list.append(ISeq(start=variant.reference_start + 1 + reference_start,
                 end=variant.reference_end + reference_start, reverse=True,weight_position=extracted.weight_position))
-        else: #bases insertion
+        elif variant.sample_end != variant.sample_start:
             seq_list.append(ISeq(sequence=sample[variant.sample_start + sample_start:variant.sample_end + sample_start],
                 weight_position=extracted.weight_position))
 

repeat-extractor.py

@@ -94,46 +94,77 @@ for line in lines:
     else:
         sequences[label] = [string.strip()]
 
+literature = {
+    'Amel':        [],
+    'CSF1P0':      ['AGAT'],
+    'D10S1248':    ['GGAA'],
+    'D12S391':     ['AGAT', 'AGAC'],
+    'D13S317':     ['TATC'],
+    'D16S539':     ['GATA'],
+    'D18S51':      ['GAAA'],
+    'D19S433':     ['AAGG'],
+    'D1S1656':     ['TAGA', 'TG'],
+    'D21S11':      ['TCTA', 'TCTG'],
+    'D22S1045':    ['ATT'],
+    'D2S1338':     ['TGCC', 'TTCC'],
+    'D2S441':      ['TCTA'],
+    'D3S1358':     ['AGAT', 'TCTA'],
+    'D5S818':      ['AGAT'],
+    'D7S820':      ['GATA'],
+    'D8S1179':     ['TATC'],
+    'FGA':         ['TTTC', 'CTTT', 'TTCC'],
+    'PentaD':      ['AAAGA'],
+    'PentaE':      ['AAAGA'],
+    'TH01':        ['TCAT'],
+    'TPOX':        ['AATG'],
+    'vWA':         ['TCTA', 'TCTG', 'TCCA'],
+    'DYS391':      ['TCTA']
+}
+
+
 #select = 'D13S317'
-#unit_list = ['TATC']
+#unit_list = literature[select]
 #reference = sequences[select][0]
-#sample = sequences[select][0]
-#description, _, _ = describe_repeats(reference, sample, unit_list)
-#print 'l.{}'.format(description)
+#sample = sequences[select][14]
+#description, rep_start, rep_end = describe_repeats(reference, sample, unit_list)
+#print '{}({}_{}):l.{}'.format(select, rep_start, rep_end, 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)
+#    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)
+
+    unit_list = literature[sequence]
 
     reference = sequences[sequence][0]
     print sequence + ':',
     print reference
-    if best > 0:
+    if len(unit_list) > 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:
+        if len(unit_list) > 0:
             description, rep_start, rep_end = describe_repeats(reference, string, unit_list)
         else:
             description = describe_dna(reference, string)