Mercurial > repos > geert-vandeweyer > cuffquant_datatype
changeset 0:f7801f8191e0 draft
Uploaded
| author | geert-vandeweyer |
|---|---|
| date | Mon, 04 Aug 2014 08:26:15 -0400 |
| parents | |
| children | e12a09256097 |
| files | README cuffquant.py datatypes_conf.xml |
| diffstat | 3 files changed, 63 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Mon Aug 04 08:26:15 2014 -0400 @@ -0,0 +1,6 @@ +## What is it? +Galaxy datatype definitions for Cuffquant output data (cxb file). Cuffquant is available starting from cufflinks 2.2.0. Wrappers are available from the toolshed. + +## Installation +Install into your local galaxy instance from the galaxy toolshed at http://testtoolshed.g2.bx.psu.edu/ or http://toolshed.g2.bx.psu.edu/ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cuffquant.py Mon Aug 04 08:26:15 2014 -0400 @@ -0,0 +1,45 @@ +""" +Cuffquant format class +""" +import logging +import re +import binascii + +from galaxy.ddatatypes.sniff import * +from galaxy.datatypes import data +from galaxy.datatypes.data import Text +from galaxy.datatypes.xml import GenericXml +from galaxy.datatypes.binary import Binary +from galaxy.datatypes.tabular import Tabular +from galaxy.datatypes.interval import Gff + +log = logging.getLogger(__name__) + +class Cuffquant( Binary ): + """Class describing a CuffQuant output file""" + file_ext = "cxb" + def sniff(self,filename): + # cuffquant cxb file is not documented. the file seems to start with 'serialization::' + try: + header = open(filename).read(23) + if header == 'serialization::': + return True + return False + except: + return False + + def set_peek( self, dataset, is_multi_byte=False): + if not dataset.dataset.purged: + dataset.peek = 'Cuffquant cxb file' + dataset.blurb = data.nice_size( dataset.get_size()) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + def display_peek (self,dataset): + try: + return dataset.peek + except: + return "Cuffquant output file (%s)" % ( data.nice_size( dataset.get_size() ) ) + +if hasattr(Binary, 'register_sniffable_binary_format'): + Binary.register_sniffable_binary_format('cxb', 'cxb', Cuffquant)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Mon Aug 04 08:26:15 2014 -0400 @@ -0,0 +1,12 @@ +<?xml version="1.0"?> +<datatypes> + <datatype_files> + <datatype_file name="cuffquant.py"/> + </datatype_files> + <registration> + <datatype extension="cxb" type="galaxy.datatypes.binary:Cuffquant" mimetype="application/octet-stream" subclass="True" display_in_upload="True" /> + </registration> + <sniffers > + <sniffer type="galaxy.datatypes.binary:Cuffquant"/> + </sniffers> +</datatypes>