Release 1.3.1

pyplink/pyplink.py

@@ -227,7 +227,7 @@ def _read_bim(self):
         # Saving the data in the object
         self._bim = bim[["chrom", "pos", "cm", "a1", "a2", "i"]]
         self._nb_markers = self._bim.shape[0]
-        self._markers = np.array(list(self._bim.index))
+        self._markers = self._bim.index.values
 
     def get_bim(self):
         """Returns the BIM file."""
@@ -346,26 +346,14 @@ def iter_geno_marker(self, markers, return_seek=False):
         if isinstance(markers, str):
             markers = [markers]
 
-        # Checking the list of required markers
-        unknown_markers = set(markers) - set(self._bim.index)
-        if len(unknown_markers) > 0:
-            raise ValueError("{}: marker not in BIM".format(
-                sorted(unknown_markers)
-            ))
-
-        # Getting the required markers
-        required_markers = self._bim.loc[markers, :]
-
-        # Then, we iterate
-        for snp, seek_position in required_markers.i.iteritems():
-            # Seeking to the correct position
-            self.seek(seek_position)
-
-            # Getting the value
-            if return_seek:
-                yield snp, self._read_current_marker(), seek_position
-            else:
-                yield snp, self._read_current_marker()
+        # Iterating over all markers
+        if return_seek:
+            for marker in markers:
+                geno, seek = self.get_geno_marker(marker, return_seek=True)
+                yield marker, geno, seek
+        else:
+            for marker in markers:
+                yield marker, self.get_geno_marker(marker)
 
     def iter_acgt_geno_marker(self, markers):
         """Iterates over genotypes for given markers (ACGT format)."""
@@ -380,7 +368,7 @@ def get_geno_marker(self, marker, return_seek=False):
             raise UnsupportedOperation("not available in 'w' mode")
 
         # Check if the marker exists
-        if marker not in set(self._bim.index):
+        if marker not in self._bim.index:
             raise ValueError("{}: marker not in BIM".format(marker))
 
         # Seeking to the correct position

pyplink/tests/test_pyplink.py

@@ -26,6 +26,7 @@
 from __future__ import print_function
 
 import os
+import sys
 import stat
 import random
 import shutil
@@ -66,10 +67,11 @@ def get_plink(tmp_dir):
         plink_path += ".exe"
 
     if find_executable(plink_path) is None:
-        print("Downloading Plink")
+        print("Downloading Plink", file=sys.stderr)
 
         # The url for each platform
-        url = "http://pngu.mgh.harvard.edu/~purcell/plink/dist/{filename}"
+        url = ("http://statgen.org/wp-content/uploads/Softwares/"
+               "plink-1.0.7/{filename}")
 
         # Getting the name of the file
         filename = ""
@@ -601,8 +603,7 @@ def test_iter_geno_marker(self):
         markers.extend(["unknown_1", "unknown_2"])
         with self.assertRaises(ValueError) as cm:
             [i for i in self.pedfile.iter_geno_marker(markers)]
-        self.assertEqual("['unknown_1', 'unknown_2']: marker not in BIM",
-                         str(cm.exception))
+        self.assertEqual("unknown_1: marker not in BIM", str(cm.exception))
 
     def test_iter_geno_marker_w_mode(self):
         """Tests that an exception is raised if in write mode."""
@@ -642,8 +643,7 @@ def test_iter_acgt_geno_marker(self):
         markers.extend(["unknown_3", "unknown_4"])
         with self.assertRaises(ValueError) as cm:
             [i for i in self.pedfile.iter_acgt_geno_marker(markers)]
-        self.assertEqual("['unknown_3', 'unknown_4']: marker not in BIM",
-                         str(cm.exception))
+        self.assertEqual("unknown_3: marker not in BIM", str(cm.exception))
 
     def test_iter_acgt_geno_marker_w_mode(self):
         """Tests that an exception is raised if in write mode."""