comparison proteomics.py @ 4:09b89b345de2

Update

3:463328a6967f

import re
from galaxy.datatypes.data import *
from galaxy.datatypes.xml import *
from galaxy.datatypes.sniff import *
from galaxy.datatypes.binary import *

log = logging.getLogger(__name__)


class Xls( Binary ):
    """Class describing a binary excel spreadsheet file"""
    file_ext = "xls"

4:09b89b345de2

import re
from galaxy.datatypes.data import *
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"""
    file_ext = "xls"