Add infrastructure for ga2vcf and ga2sam tools

Does not close ga4gh#83

ga2sam_dev.py

@@ -0,0 +1,11 @@
+"""
+Shim for running the ga2sam tool during development
+"""
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
+
+import ga4gh.cli
+
+if __name__ == "__main__":
+    ga4gh.cli.ga2sam_main()

ga2vcf_dev.py

@@ -0,0 +1,11 @@
+"""
+Shim for running the ga2vcf tool during development
+"""
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
+
+import ga4gh.cli
+
+if __name__ == "__main__":
+    ga4gh.cli.ga2vcf_main()

ga4gh/cli.py

@@ -9,12 +9,68 @@
 
 import time
 import argparse
+import sys
 
 import ga4gh.frontend as frontend
 import ga4gh.client as client
 import ga4gh.backend as backend
 import ga4gh.protocol as protocol
 import ga4gh.datamodel.variants as variants
+import ga4gh.converters as converters
+
+
+##############################################################################
+# ga2vcf
+##############################################################################
+
+
+def ga2vcf_main(parser=None):
+    if parser is None:
+        parser = argparse.ArgumentParser(
+            description="GA4GH VCF conversion tool")
+    addClientGlobalOptions(parser)
+    subparsers = parser.add_subparsers(title='subcommands',)
+    addVariantsSearchParser(subparsers)
+    args = parser.parse_args()
+    request = protocol.GASearchVariantsRequest()
+    setCommaSeparatedAttribute(request, args, 'datasetIds')
+    # TODO add outputFile cli argument
+    outputFile = sys.stdout
+    vcfConverter = converters.VcfConverter(request, outputFile)
+    vcfConverter.convert()
+
+
+##############################################################################
+# ga2sam
+##############################################################################
+
+
+def ga2sam_main(parser=None):
+
+    def usingWorkaroundsFor(workaround):
+        return workaround in workarounds
+
+    if parser is None:
+        parser = argparse.ArgumentParser(
+            description="GA4GH SAM conversion tool")
+    addClientGlobalOptions(parser)
+    subparsers = parser.add_subparsers(title='subcommands',)
+    addReadsSearchParser(subparsers)
+    args = parser.parse_args()
+    workarounds = set(args.workarounds.split(','))
+    request = protocol.GASearchReadsRequest()
+    if usingWorkaroundsFor(client.HttpClient.workaroundGoogle):
+        # google says referenceId not a valid field
+        request = SearchReadsRunner.GASearchReadsRequestGoogle()
+    setCommaSeparatedAttribute(request, args, 'readGroupIds')
+    request.start = args.start
+    request.end = args.end
+    request.referenceId = args.referenceId
+    request.referenceName = args.referenceName
+    # TODO add outputFile cli argument
+    outputFile = sys.stdout
+    samConverter = converters.SamConverter(request, outputFile)
+    samConverter.convert()
 
 
 def setCommaSeparatedAttribute(request, args, attr):

ga4gh/converters.py

@@ -0,0 +1,40 @@
+"""
+Provides classes that take protocol requests, send that request to
+the server, and write a particular genomics file type with the results.
+"""
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
+
+
+class AbstractConverter(object):
+    """
+    Abstract base class for converter classes
+    """
+    def __init__(self, request, outputStream):
+        self._request = request
+        self._outputStream = outputStream
+
+
+class SamConverter(AbstractConverter):
+    """
+    Converts a request to a SAM file
+    """
+    def __init__(self, searchReadsRequest, outputStream):
+        super(SamConverter, self).__init__(
+            searchReadsRequest, outputStream)
+
+    def convert(self):
+        raise NotImplementedError()
+
+
+class VcfConverter(AbstractConverter):
+    """
+    Converts a request to a VCF file
+    """
+    def __init__(self, searchVariantsRequest, outputStream):
+        super(VcfConverter, self).__init__(
+            searchVariantsRequest, outputStream)
+
+    def convert(self):
+        raise NotImplementedError()

setup.py

@@ -46,6 +46,8 @@ def parseVersion(moduleFile):
         'console_scripts': [
             'ga4gh_client=ga4gh.cli:client_main',
             'ga4gh_server=ga4gh.cli:server_main',
+            'ga2vcf=ga4gh.cli:ga2vcf_main',
+            'ga2sam=ga4gh.cli:ga2sam_main',
         ]
     },
     classifiers=[