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Commit message:
planemo upload commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty |
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added:
datatypes_conf.xml oxli.py |
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| diff -r 000000000000 -r 3641a7d3b7c4 datatypes_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Tue Jul 07 12:27:08 2015 -0400 |
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| @@ -0,0 +1,16 @@ +<?xml version="1.0"?> +<datatypes> + <datatype_files> + <datatype_file name="oxli.py"/> + </datatype_files> + <registration> + <datatype extension="ct" type="galaxy.datatypes.oxli:Count" + mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="pt" type="galaxy.datatypes.oxli:Presence" + mimetype="application/octet-stream" display_in_upload="true"/> + </registration> + <sniffers> + <sniffer type="galaxy.datatypes.oxli:Count"/> + <sniffer type="galaxy.datatypes.oxli:Presence"/> + </sniffers> +</datatypes> |
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| diff -r 000000000000 -r 3641a7d3b7c4 oxli.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/oxli.py Tue Jul 07 12:27:08 2015 -0400 |
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| @@ -0,0 +1,51 @@ +""" +k-mer count and presence +""" + +from galaxy.datatypes.binary import Binary +import binascii + +import logging + +log = logging.getLogger(__name__) + + +class OxliBinary(Binary): + + def __init__(self, **kwd): + Binary.__init__(self, **kwd) + + def sniff(self, filename, filetype): + try: + with open(filename) as fileobj: + header = fileobj.read(4) + if binascii.b2a_hex(header) == binascii.hexlify('OXLI'): + fileobj.seek(1) + ftype = fileobj.read(1) + if binascii.b2a_hex(ftype) == filetype: + return True + return False + except IOError: + return False + + +class Count(OxliBinary): + + def __init__(self, **kwd): + OxliBinary.__init__(self, **kwd) + + def sniff(self, filename): + return OxliBinary.sniff(self, filename, "01") + + +class Presence(OxliBinary): + + def __init__(self, **kwd): + OxliBinary.__init__(self, **kwd) + + def sniff(self, filename): + return OxliBinary.sniff(self, filename, "02") + + +Binary.register_sniffable_binary_format("ct", "ct", Count) +Binary.register_sniffable_binary_format("pt", "pt", Presence) |