Added a wig file parser.

gepyto/formats/wig.py

@@ -0,0 +1,120 @@
+"""
+Parser for Wiggle Track Format files.
+"""
+
+# This file is part of gepyto.
+#
+# This work is licensed under the Creative Commons Attribution-NonCommercial
+# 4.0 International License. To view a copy of this license, visit
+# http://creativecommons.org/licenses/by-nc/4.0/ or send a letter to Creative
+# Commons, PO Box 1866, Mountain View, CA 94042, USA.
+
+__author__ = "Marc-Andre Legault"
+__copyright__ = ("Copyright 2014 Marc-Andre Legault and Louis-Philippe "
+                 "Lemieux Perreault. All rights reserved.")
+__license__ = "Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"
+
+
+import os
+
+import pandas as pd
+import six
+
+from ..structures.region import _Segment, Region
+
+
+
+class WiggleFile(object):
+    """Parser for WIG files.
+    
+    This returns a pandas dataframe with all the necessary information. In the
+    process, all the inherent compactness of the Wiggle format is lost in
+    exchange for an easier to manage representation. This means that more
+    efficient parsers should be used for large chunks of data.
+
+    """
+    def __init__(self, stream):
+        self.stream = stream
+        if isinstance(stream, six.string_types):
+            if os.path.isfile(stream):
+                self.stream = open(stream, "r")
+            else:
+                raise IOError("Can't find file '{}'.".format(stream))
+
+        mode, first_header = self._parse_header(next(self.stream))
+        if mode == "fixedStep":
+            self.data = self._parse_fixed_step(header=first_header)
+        else:
+            raise NotImplementedError("fixedStep is the only implemented mode "
+                                      "for now.")
+
+        # Use categories for chrom to save space.
+        self.data["chrom"] = self.data["chrom"].astype("category")
+
+        # Check if regions or only 1 bases
+        # If so use pos instead of start, end.
+        if (self.data["start"] == self.data["end"]).all():
+            self.data = self.data.drop("end", axis=1)
+            self.data.columns = ("chrom", "pos", "value")
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, *params):
+        self.close()
+
+    def close(self):
+        # This will close the file if it's a file.
+        try:
+            self.stream.close()
+        except AttributeError:
+            pass
+
+    def as_dataframe(self):
+        return self.data
+
+
+    def _parse_fixed_step(self, header=None):
+        data = []
+        for line in self.stream:
+            if self._is_header(line):
+                mode, header = self._parse_header(line)
+                assert (
+                    mode == "fixedStep"
+                ), "Can't change mode after parsing started."
+
+            else:
+                data.append((
+                    header["chrom"],
+                    header["pos"],
+                    header["pos"] + header["span"] - 1,
+                    float(line.rstrip())
+                ))
+                header["pos"] += header["step"]
+
+        return pd.DataFrame(
+            data,
+            columns=("chrom", "start", "end", "value")
+        )
+
+
+    @staticmethod
+    def _parse_header(line):
+        line = line.rstrip().split()
+        mode = line[0]
+
+        line = line[1:]
+        header = dict([field.split("=") for field in line])
+        header["start"] = int(header["start"])
+        header["step"] = int(header["step"])
+        header["span"] = int(header.get("span", 1))
+
+        header["pos"] = header["start"]
+
+        return mode, header
+
+    @staticmethod
+    def _is_header(line):
+        return (
+            line.startswith("variableStep") or line.startswith("fixedStep")
+        )

gepyto/structures/region.py

@@ -13,14 +13,15 @@
                  "Lemieux Perreault. All rights reserved.")
 __license__ = "Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"
 
-__all__ = ["Region", "get_centromere", "get_telomere"]
-
 
 import re
 
 from .. import settings
 from . import sequences
 
+import numpy as np
+from six.moves import range
+
 
 class _Segment(object):
     def __init__(self, chrom, start, end):
@@ -46,6 +47,11 @@ def distance_to(self, segment):
         else:
             return self.start - segment.end
 
+    def as_range(self, iterator=False):
+        if iterator:
+            return range(self.start, self.end + 1)
+        return np.arange(self.start, self.end + 1)
+
     def __eq__(self, seg):
         return (self.chrom == seg.chrom and self.start == seg.start and
                 self.end == seg.end)
@@ -171,6 +177,13 @@ def distance_to(self, region):
                     min_dist = d
         return min_dist
 
+    def as_range(self, iterator=False):
+        """Get a range corresponding to all the nucleotide positions."""
+        if self.is_contiguous:
+            return self.segments[0].as_range(iterator)
+        else:
+            return set([seg.as_range(iterator) for seg in self.segments])
+
     @property
     def chrom(self):
         if self.is_contiguous: