changeset 11:cb443c64ebad draft

Deleted selected files

--- a/vcfs2fasta/phe/variant/MPileupVariantCaller.py	Wed Dec 16 07:25:33 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,96 +0,0 @@
-'''
-Created on 22 Sep 2015
-
-@author: alex
-'''
-from collections import OrderedDict
-import logging
-import os
-import subprocess
-import tempfile
-
-from phe.variant import VariantCaller
-
-
-class MPileupVariantCaller(VariantCaller):
-    """Implemetation of the Broad institute's variant caller."""
-
-    name = "mpileup"
-    """Plain text name of the variant caller."""
-
-    _default_options = "-m -f GQ"
-    """Default options for the variant caller."""
-
-    def __init__(self, cmd_options=None):
-        """Constructor"""
-        if cmd_options is None:
-            cmd_options = self._default_options
-
-        super(MPileupVariantCaller, self).__init__(cmd_options=cmd_options)
-
-        self.last_command = None
-
-    def get_info(self, plain=False):
-        d = {"name": self.name, "version": self.get_version(), "command": self.last_command}
-
-        if plain:
-            result = "mpileup(%(version)s): %(command)s" % d
-        else:
-            result = OrderedDict(d)
-
-        return result
-
-    def get_version(self):
-
-        p = subprocess.Popen(["samtools", "--version"], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
-        (output, _) = p.communicate()
-
-        # first line is the version of the samtools
-        version = output.split("\n")[0].split(" ")[1]
-
-        return version
-
-    def make_vcf(self, *args, **kwargs):
-        ref = kwargs.get("ref")
-        bam = kwargs.get("bam")
-
-        if kwargs.get("vcf_file") is None:
-            kwargs["vcf_file"] = "variants.vcf"
-
-        opts = {"ref": os.path.abspath(ref),
-                "bam": os.path.abspath(bam),
-                "all_variants_file": os.path.abspath(kwargs.get("vcf_file")),
-                "extra_cmd_options": self.cmd_options}
-
-        with tempfile.NamedTemporaryFile(suffix=".pileup") as tmp:
-            opts["pileup_file"] = tmp.name
-            cmd = "samtools mpileup -t DP,DV,DP4,DPR,SP -Auf %(ref)s %(bam)s | bcftools call %(extra_cmd_options)s > %(all_variants_file)s" % opts
-            print cmd
-            self.last_command = cmd
-            if os.system(cmd) != 0:
-                logging.warn("Pileup creation was not successful.")
-                return False
-
-        return True
-
-    def create_aux_files(self, ref):
-        """Index reference with faidx from samtools.
-
-        Parameters:
-        -----------
-        ref: str
-            Path to the reference file.
-
-        Returns:
-        --------
-        bool:
-            True if auxiliary files were created, False otherwise.
-        """
-
-        success = os.system("samtools faidx %s" % ref)
-
-        if success != 0:
-            logging.warn("Fasta index could not be created.")
-            return False
-
-        return True