diff phe/variant/GATKVariantCaller.py @ 22:96f393ad7fc6 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant/GATKVariantCaller.py	Wed Dec 23 04:50:58 2015 -0500
@@ -0,0 +1,133 @@
+'''
+Created on 22 Sep 2015
+
+@author: alex
+'''
+from collections import OrderedDict
+import logging
+import os
+import subprocess
+
+from phe.variant import VariantCaller
+
+
+class GATKVariantCaller(VariantCaller):
+    """Implemetation of the Broad institute's variant caller."""
+
+    name = "gatk"
+    """Plain text name of the variant caller."""
+
+    _default_options = "--sample_ploidy 2 --genotype_likelihoods_model BOTH -rf BadCigar -out_mode EMIT_ALL_SITES -nt 1"
+    """Default options for the variant caller."""
+
+    def __init__(self, cmd_options=None):
+        """Constructor"""
+        if cmd_options is None:
+            cmd_options = self._default_options
+
+        super(GATKVariantCaller, self).__init__(cmd_options=cmd_options)
+
+        self.last_command = None
+
+    def get_info(self, plain=False):
+        d = {"name": "gatk", "version": self.get_version(), "command": self.last_command}
+
+        if plain:
+            result = "GATK(%(version)s): %(command)s" % d
+        else:
+            result = OrderedDict(d)
+
+        return result
+
+    def get_version(self):
+
+        p = subprocess.Popen(["java", "-jar", os.environ["GATK_JAR"], "-version"], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+        (output, _) = p.communicate()
+
+        # last character is EOL.
+        version = output.split("\n")[-2]
+
+        return version
+
+    def make_vcf(self, *args, **kwargs):
+        ref = kwargs.get("ref")
+        bam = kwargs.get("bam")
+
+        make_aux = kwargs.get("make_aux", False)
+
+        if kwargs.get("vcf_file") is None:
+            kwargs["vcf_file"] = "variants.vcf"
+
+        opts = {"ref": os.path.abspath(ref),
+                "bam": os.path.abspath(bam),
+                "gatk_jar": os.environ["GATK_JAR"],
+                "all_variants_file": os.path.abspath(kwargs.get("vcf_file")),
+                "extra_cmd_options": self.cmd_options}
+        if make_aux:
+            if not self.create_aux_files(ref):
+                logging.warn("Auxiliary files were not created.")
+                return False
+
+        # Call variants
+        # FIXME: Sample ploidy = 2?
+        os.environ["GATK_JAR"]
+        cmd = "java -XX:+UseSerialGC -jar %(gatk_jar)s -T UnifiedGenotyper -R %(ref)s -I %(bam)s -o %(all_variants_file)s %(extra_cmd_options)s" % opts
+        success = os.system(cmd)
+
+        if success != 0:
+            logging.warn("Calling variants returned non-zero exit status.")
+            return False
+
+        self.last_command = cmd
+
+        return True
+
+    def create_aux_files(self, ref):
+        """Create auxiliary files needed for this variant.
+
+        Tools needed: samtools and picard tools. Picard tools is a Java
+        library that can be defined using environment variable: PICARD_JAR
+        specifying path to picard.jar or PICARD_TOOLS_PATH specifying path
+        to the directory where separate jars are (older version before jars
+        were merged into a single picard.jar).
+        Parameters:
+        -----------
+        ref: str
+            Path to the reference file.
+        
+        Returns:
+        --------
+        bool:
+            True if auxiliary files were created, False otherwise.
+        """
+
+        ref_name, _ = os.path.splitext(ref)
+
+        success = os.system("samtools faidx %s" % ref)
+
+        if success != 0:
+            logging.warn("Fasta index could not be created.")
+            return False
+
+        d = {"ref": ref, "ref_name": ref_name}
+
+        if os.environ.get("PICARD_TOOLS_PATH"):
+            d["picard_tools_path"] = os.path.join(os.environ["PICARD_TOOLS_PATH"], "CreateSequenceDictionary.jar")
+        elif os.environ.get("PICARD_JAR"):
+            # This is used in newer version of PICARD tool where multiple
+            #    jars were merged into a single jar file.
+            d["picard_tools_path"] = "%s %s" % (os.environ["PICARD_JAR"], "CreateSequenceDictionary")
+        else:
+            logging.error("Picard tools are not present in the path.")
+            return False
+
+        if not os.path.exists("%s.dict" % ref_name):
+            success = os.system("java -jar %(picard_tools_path)s R=%(ref)s O=%(ref_name)s.dict" % d)
+
+            if success != 0:
+                logging.warn("Dictionary for the %s reference could not be created", ref)
+                return False
+        else:
+            logging.debug("PICARD AUX EXISTS.")
+
+        return True