From 0beac8fdf4835271ccafefd6a50f928afa055c2c Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Thu, 1 Nov 2018 23:46:41 +0100
Subject: [PATCH] rma: add RMA6 data type (MEGAN6 read-match archive)

---
 config/datatypes_conf.xml.sample      |   2 ++
 lib/galaxy/datatypes/binary.py        |  23 +++++++++++++++++++++++
 lib/galaxy/datatypes/test/diamond.rma | Bin 0 -> 1447 bytes
 3 files changed, 25 insertions(+)
 create mode 100644 lib/galaxy/datatypes/test/diamond.rma

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 9f054936e65..4e38c97b638 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -54,6 +54,7 @@
       <converter file="len_to_linecount.xml" target_datatype="linecount"/>
     </datatype>
     <datatype extension="daa" type="galaxy.datatypes.binary:DAA" display_in_upload="true"/>
+    <datatype extension="rma" type="galaxy.datatypes.binary:RMA" display_in_upload="true"/>
     <datatype extension="dmnd" type="galaxy.datatypes.binary:DMND" display_in_upload="false"/>
     <datatype extension="idat" type="galaxy.datatypes.binary:Idat" display_in_upload="true"/>
     <datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" display_in_upload="true">
@@ -734,6 +735,7 @@
     <sniffer type="galaxy.datatypes.binary:Sra"/>
     <sniffer type="galaxy.datatypes.binary:NetCDF"/>
     <sniffer type="galaxy.datatypes.binary:DAA"/>
+    <sniffer type="galaxy.datatypes.binary:RMA"/>
     <sniffer type="galaxy.datatypes.binary:DMND"/>
     <sniffer type="galaxy.datatypes.binary:Fast5ArchiveGz"/>
     <sniffer type="galaxy.datatypes.binary:Fast5ArchiveBz2"/>
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index c4189b28ce1..5fed1320953 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -2168,6 +2168,29 @@ class DAA(Binary):
             return f.read(8) == self._magic
 
 
+class RMA6(Binary):
+    """
+    Class describing an RMA6 (MEGAN6 read-match archive) file
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('diamond.rma')
+    >>> DAA().sniff(fname)
+    True
+    >>> fname = get_test_fname('interval.interval')
+    >>> DAA().sniff(fname)
+    False
+    """
+    file_ext = "rma6"
+
+    def __init__(self, **kwd):
+        Binary.__init__(self, **kwd)
+        self._magic = binascii.unhexlify("000003f600000006")
+
+    def sniff(self, filename):
+        # The first 8 bytes of any daa file are 0x3c0e53476d3ee36b
+        with open(filename, 'rb') as f:
+            return f.read(8) == self._magic
+
+
 class DMND(Binary):
     """
     Class describing an DMND file
diff --git a/lib/galaxy/datatypes/test/diamond.rma b/lib/galaxy/datatypes/test/diamond.rma
new file mode 100644
index 0000000000000000000000000000000000000000..abc824d7e0103a92f37b05bc6a3c1393127cb373
GIT binary patch
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literal 0
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