Merge pull request #1148 from markiskander/bcfgz_to_bcf_converter

Bcf.gz to bcf (and reverse) converters + bcf_bgzip data type

config/datatypes_conf.xml.sample

@@ -247,7 +247,12 @@
       <display file="igv/vcf.xml" />
       <display file="rviewer/vcf.xml" inherit="True"/>
     </datatype>
-    <datatype extension="bcf" type="galaxy.datatypes.binary:Bcf" mimetype="application/octet-stream" display_in_upload="True"/>
+    <datatype extension="bcf" type="galaxy.datatypes.binary:Bcf" mimetype="application/octet-stream" display_in_upload="True">
+      <converter file="bcf_to_bcf_bgzip_converter.xml" target_datatype="bcf_bgzip"/>
+    </datatype>
+    <datatype extension="bcf_bgzip" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True">
+      <converter file="bcf_bgzip_to_bcf_converter.xml" target_datatype="bcf"/>
+    </datatype>
     <datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/>
     <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true" description="The wiggle format is line-oriented.  Wiggle data is preceded by a track definition line, which adds a number of options for controlling the default display of this track." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Wig">
       <converter file="wig_to_bigwig_converter.xml" target_datatype="bigwig"/>

doc/source/lib/galaxy.datatypes.converters.rst

@@ -225,6 +225,22 @@ galaxy.datatypes.converters.vcf_to_vcf_bgzip module
     :undoc-members:
     :show-inheritance:
 
+galaxy.datatypes.converters.bcf_bgzip_to_bcf module
+---------------------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.bcf_bgzip_to_bcf
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+galaxy.datatypes.converters.bcf_to_bcf_bgzip module
+---------------------------------------------------
+
+.. automodule:: galaxy.datatypes.converters.bcf_to_bcf_bgzip
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 galaxy.datatypes.converters.wiggle_to_array_tree_converter module
 -----------------------------------------------------------------
 
@@ -240,5 +256,3 @@ galaxy.datatypes.converters.wiggle_to_simple_converter module
     :members:
     :undoc-members:
     :show-inheritance:
-
-

lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python
+
+"""
+Uses bcftools to extract a bcf from a bcf.gz
+
+usage: %prog in_file out_file
+"""
+import optparse
+import subprocess
+
+
+def main():
+    # Read options, args.
+    parser = optparse.OptionParser()
+    (options, args) = parser.parse_args()
+    input_fname, output_fname = args
+
+    subprocess.call(["bcftools", "view", input_fname, "-o", output_fname, "-O", "u"])
+
+
+if __name__ == "__main__":
+    main()

lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml

@@ -0,0 +1,14 @@
+<tool id="CONVERTER_bcf_bgzip_to_bcf" name="Convert BCF_BGZIP to BCF" version="0.0.1" hidden="false">
+<!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+  <command interpreter="python">bcf_bgzip_to_bcf_converter.py '$input1' '$output1'</command>
+  <inputs>
+    <page>
+        <param format="bcf_bgzip" name="input1" type="data" label="Choose bcf_bgzip file"/>
+    </page>
+   </inputs>
+  <outputs>
+    <data format="bcf" name="output1"/>
+  </outputs>
+  <help>
+  </help>
+</tool>

lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python
+
+"""
+Uses bcftools to compress a bcf into a bcf.gz
+
+usage: %prog in_file out_file
+"""
+import optparse
+import subprocess
+
+
+def main():
+    # Read options, args.
+    parser = optparse.OptionParser()
+    (options, args) = parser.parse_args()
+    input_fname, output_fname = args
+
+    subprocess.call(["bcftools", "view", input_fname, "-o", output_fname, "-O", "b"])
+
+
+if __name__ == "__main__":
+    main()

lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml

@@ -0,0 +1,14 @@
+<tool id="CONVERTER_bcf_to_bcf_bgzip" name="Convert BCF to BCF_BGZIP" version="0.0.1" hidden="false">
+<!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+  <command interpreter="python">bcf_to_bcf_bgzip_converter.py '$input1' '$output1'</command>
+  <inputs>
+    <page>
+        <param format="bcf" name="input1" type="data" label="Choose bcf file"/>
+    </page>
+   </inputs>
+  <outputs>
+    <data format="bcf_bgzip" name="output1"/>
+  </outputs>
+  <help>
+  </help>
+</tool>