Command line wrapper for BWA

This is a squashed commit based on Saket's pull request,
rebased after making similar enhancements to the __call__
method of the base class for stdout/stderr as filenames.

Bio/Align/Applications/__init__.py

@@ -23,5 +23,5 @@
            "MafftCommandline",
            "DialignCommandline",
            "ProbconsCommandline",
-           "TCoffeeCommandline",
+           "TCoffeeCommandline"
            ]

Bio/Sequencing/Applications/__init__.py

@@ -1,3 +1,11 @@
 """Main entry point for application command line wrappers related to sequencing.
 """
 from _Novoalign import NovoalignCommandline
+from _bwa import BwaIndexCommandline,BwaAlignCommandline,BwaSamseCommandline,BwaSampeCommandline,BwaBwaswCommandline
+#Make this explicit, then they show up in the API docs
+__all__ = ["BwaIndexCommandline",
+           "BwaAlignCommandline",
+           "BwaSamseCommandline",
+           "BwaSampeCommandline",
+           "BwaBwaswCommandline"
+           ]

Tests/test_BWA_tool.py

@@ -0,0 +1,137 @@
+# Copyright 2013 by Saket Choudhary.  Based on test_Clustalw_tool.py by Peter
+# Cock .
+#
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+
+from Bio import MissingExternalDependencyError
+import sys
+import os
+import unittest
+from Bio import SeqIO
+from Bio import AlignIO
+from Bio.Sequencing.Applications import BwaIndexCommandline, BwaAlignCommandline, BwaSamseCommandline, BwaSampeCommandline, BwaBwaswCommandline
+from Bio.Application import ApplicationError
+
+#################################################################
+
+#Try to avoid problems when the OS is in another language
+os.environ['LANG'] = 'C'
+
+clustalw_exe = None
+if sys.platform == "win32":
+    #TODO - Check the path?
+    try:
+        #This can vary depending on the Windows language.
+        prog_files = os.environ["PROGRAMFILES"]
+    except KeyError:
+        prog_files = r"C:\Program Files"
+    #A default path of C:\Program Files\bwa.exe was chosen
+    #but this path can be edited depending on where bwa is located
+
+    likely_dirs = ["bwa", "BWA", "Bwa", "bwa-0.6.2"]
+    likely_exes = ["bwa.exe", "BWA.exe", "Bwa.exe"]
+    for folder in likely_dirs:
+        if os.path.isdir(os.path.join(prog_files, folder)):
+            for filename in likely_exes:
+                if os.path.isfile(os.path.join(prog_files, folder, filename)):
+                    bwa_exe = os.path.join(prog_files, folder, filename)
+                    break
+            if bwa_exe:
+                break
+else:
+    import commands
+    output = commands.getoutput("bwa")
+
+    #Since "not found" may be in another language, try and be sure this is
+    #really the bwa tool's output
+    bwa_found = False
+    if "not found" not in output and "bwa" in output \
+    and "alignment via Burrows-Wheeler transformation" in output:
+        bwa_exe = "bwa"
+
+if not bwa_exe:
+    raise MissingExternalDependencyError(\
+        "Install bwa and correctly set the file path to the program if you want to use it from Biopython")
+
+
+class BwaTestCase(unittest.TestCase):
+    """Class for implementing BWA test cases"""
+    def setUp(self):
+        self.reference_file = os.path.join(os.path.dirname(os.path.abspath(__file__)),"BWA", "human_g1k_v37_truncated.fasta")
+        self.infile1 = os.path.join(os.path.dirname(os.path.abspath(__file__)),"BWA", "HNSCC1_1_truncated.fastq")
+        self.infile2 = os.path.join(os.path.dirname(os.path.abspath(__file__)),"BWA", "HNSCC1_2_truncated.fastq")
+        self.saifile1 = os.path.join(os.path.dirname(os.path.abspath(__file__)),"BWA" ,"1.sai")
+        self.saifile2 = os.path.join(os.path.dirname(os.path.abspath(__file__)),"BWA", "2.sai")
+        self.samfile1 = os.path.join(os.path.dirname(os.path.abspath(__file__)),"BWA" ,"1.sam")
+        self.samfile2 = os.path.join(os.path.dirname(os.path.abspath(__file__)),"BWA", "2.sam")
+        self.samfile = os.path.join(os.path.dirname(os.path.abspath(__file__)),"BWA", "out.sam")
+
+    def test_index(self):
+        """Test for creating index files for the reference genome fasta file"""
+        cmdline = BwaIndexCommandline()
+        cmdline.set_parameter("infile", self.reference_file)
+        cmdline.set_parameter("algorithm","bwtsw")
+        stdout,stderr = cmdline()
+        output = stdout.startswith("[bwt_gen]")
+        self.assertEqual(True, output, "FASTA indexing failed")
+
+    def test_aln(self, paired_end=False):
+        """Test for generating sai files given the reference and read file"""
+        cmdline = BwaAlignCommandline()
+        cmdline.set_parameter("reference", self.reference_file)
+        if not paired_end:
+            cmdline.set_parameter("read_file", self.infile1)
+            stdout, stderr = cmdline(stdout=self.saifile1)
+        else:
+            cmdline.set_parameter("read_file", self.infile2)
+            stdout, stderr = cmdline(stdout=self.saifile2)
+
+        if "fail to locate the index" in stderr:
+            output = False
+        else:
+            output = True
+        self.assertEqual(True, output, "Error aligning sequence to reference")
+
+    def test_samse(self):
+        """Test for single end sequencing """
+        cmdline = BwaSamseCommandline()
+        cmdline.set_parameter("reference", self.reference_file)
+        cmdline.set_parameter("read_file", self.infile1)
+        cmdline.set_parameter("sai_file", self.saifile1)
+        stdout, stderr = cmdline(stdout=self.samfile1)
+
+        headline = open(self.samfile1, "r").readline()
+        if headline.startswith("@SQ"):
+            output = True
+        else:
+            output = False
+        self.assertEqual(True, output, "Error generating sam files")
+
+    def test_sampe(self):
+        """Test for generating samfile by paired end sequencing"""
+        ##Generate sai files from paired end data
+        self.test_aln(True)
+        self.test_aln(False)
+
+        cmdline = BwaSampeCommandline()
+        cmdline.set_parameter("reference", self.reference_file)
+        cmdline.set_parameter("sai_file1", self.saifile1)
+        cmdline.set_parameter("sai_file2", self.saifile2)
+        cmdline.set_parameter("read_file1", self.infile1)
+        cmdline.set_parameter("read_file2", self.infile2)
+        stdout, stderr = cmdline(stdout=self.samfile)
+
+        headline = open(self.samfile, "r").readline()
+        if headline.startswith("@SQ"):
+            output = True
+        else:
+            output = False
+        self.assertEqual(True, output, "Error generating sam files")
+
+
+
+if __name__ == "__main__":
+    runner = unittest.TextTestRunner(verbosity = 2)
+    unittest.main(testRunner=runner)