| Previous changeset 3:463328a6967f (2013-03-04) Next changeset 5:df8b867ab71a (2014-02-07) |
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Commit message:
Update |
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modified:
datatypes_conf.xml proteomics.py |
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| diff -r 463328a6967f -r 09b89b345de2 datatypes_conf.xml --- a/datatypes_conf.xml Mon Mar 04 19:00:50 2013 -0500 +++ b/datatypes_conf.xml Sun Jun 09 08:16:08 2013 -0500 |
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| @@ -3,7 +3,10 @@ <datatype_files> <datatype_file name="proteomics.py"/> </datatype_files> - <registration display_path="display_applications"> + <registration display_path="display_applications"> + <datatype extension="prot_gff" type="galaxy.datatypes.proteomics:ProtGff" mimetype="application/xml" display_in_upload="true"> + <display file="proteomics/ProtGff.xml" /> + </datatype> <datatype extension="pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" display_in_upload="true"> <display file="proteomics/PepXml.xml" /> </datatype> @@ -35,6 +38,7 @@ <datatype extension="hlf" type="galaxy.datatypes.proteomics:XHunterAslFormat" display_in_upload="true" /> </registration> <sniffers> + <sniffer type="galaxy.datatypes.proteomics:ProtGff"/> <sniffer type="galaxy.datatypes.proteomics:MzML"/> <sniffer type="galaxy.datatypes.proteomics:PepXml"/> <sniffer type="galaxy.datatypes.proteomics:Mgf"/> |
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| diff -r 463328a6967f -r 09b89b345de2 proteomics.py --- a/proteomics.py Mon Mar 04 19:00:50 2013 -0500 +++ b/proteomics.py Sun Jun 09 08:16:08 2013 -0500 |
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| @@ -7,9 +7,34 @@ from galaxy.datatypes.xml import * from galaxy.datatypes.sniff import * from galaxy.datatypes.binary import * +from galaxy.datatypes.interval import * log = logging.getLogger(__name__) +class ProtGff( Gff ): + """Tab delimited data in Gff format""" + file_ext = "prot_gff" + def set_peek( self, dataset, is_multi_byte=False ): + """Set the peek and blurb text""" + if not dataset.dataset.purged: + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + dataset.blurb = 'Proteogenomics GFF' + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + def sniff( self, filename ): + handle = open(filename) + xmlns_re = re.compile("^##gff-version") + for i in range(3): + line = handle.readline() + if xmlns_re.match(line.strip()): + handle.close() + return True + + handle.close() + return False + class Xls( Binary ): """Class describing a binary excel spreadsheet file""" |