diff rois.py @ 0:61d9bdb6d519 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rois.py	Thu Apr 18 08:03:38 2013 -0400
@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+
+class RoiRecord(object):
+    """Represent one record in a ROI file."""
+
+    def __init__(self, ref, start_pos, end_pos, region_name, region_length,
+                 strand, max_count, data, points):
+        """Initialize RoiRecord."""
+        self.ref = ref
+        self.start_pos = start_pos
+        self.end_pos = end_pos
+        self.strand = strand
+        self.region_length = region_length
+        self.region_name = region_name
+        self.max_count = max_count
+        self.data = data
+        self.points = points
+
+    def __str__(self):
+        return 'RoiRecord(%s, %s, %s, %s, %s, %s, %s, %s, len([...])==%s)' % \
+                   (repr(self.ref), self.start_pos, self.end_pos,
+                    self.region_name, self.region_length, repr(self.strand),
+                    self.max_count, self.data, len(self.points))
+    def __repr__(self):
+        return self.__str__()
+
+
+def loadRoi(path, max_count=0):
+    """Load ROI file and return it as a list of RoiRecord objects.
+
+    NA values are translated to 0.
+    """
+    data_keys = []
+    result = []
+    i = 0
+    with open(path, 'rb') as f:
+        for line in f:
+            if line.startswith('##'):
+                data_keys = line[2:].split('\t')[7:-1]
+            if line[0] == '#':
+                continue
+            if max_count > 0 and i >= max_count:
+                break
+            i += 1
+            vals = line.split()
+            region_length = int(vals[4])
+            data = vals[7:-1]
+            points = [int(x) for x in vals[-1].split(',')]
+            r = RoiRecord(vals[0], int(vals[1]) - 1, int(vals[2]), vals[3],
+                         region_length, vals[5], int(vals[6]), data, points)
+            result.append(r)
+    #print '  => Loaded %d records.' % len(result)
+    return data_keys, result