diff wiggle.py @ 0:e8475d0195fe draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wiggle.py	Wed Mar 01 22:47:20 2017 -0500
@@ -0,0 +1,55 @@
+class Wiggle:
+
+    def fixedStepParser(self, line):
+        value = line.strip()
+        start_position = self.stepIdx * self.parserConfig['step'] + self.parserConfig['start']
+        stop_position = start_position + self.parserConfig['span'] - 1
+        self.stepIdx += 1
+
+        for position in xrange(start_position, stop_position):
+            yield (self.parserConfig['chrom'], position, value)
+
+    def variableStepParser(self, line):
+        (start, value) = line.strip().split()
+        start = int(start)
+        start_position = start
+        stop_position = start + self.parserConfig['span']
+
+        for position in xrange(start_position, stop_position):
+            yield (self.parserConfig['chrom'], position, value)
+
+    def walk(self, handle):
+
+        parser = None
+        for line in handle:
+            if line.startswith('track'):
+                continue
+            elif line.startswith('fixedStep'):
+                parser = self.fixedStepParser
+                lineData = line.split()
+                fields = {x.split('=')[0]: x.split('=')[1] for x in lineData[1:]}
+                self.parserConfig = fields
+
+                for numField in ('step', 'start', 'span'):
+                    if numField in self.parserConfig:
+                        self.parserConfig[numField] = int(self.parserConfig[numField])
+                self.stepIdx = 0
+            elif line.startswith('variableStep'):
+                parser = self.variableStepParser
+                lineData = line.split()
+                fields = {x.split('=')[0]: x.split('=')[1] for x in lineData[1:]}
+                # Default value
+                if 'span' not in fields:
+                    fields['span'] = 1
+                self.parserConfig = fields
+
+                for numField in ('span',):
+                    if numField in self.parserConfig:
+                        self.parserConfig[numField] = int(self.parserConfig[numField])
+
+                self.stepIdx = 0
+            elif len(line.strip()) == 0:
+                continue
+            else:
+                for data in parser(line):
+                    yield data