comparison mothur/lib/galaxy/datatypes/metagenomics.py @ 26:5c77423823cb

Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)

25:bfbaf823be4c

from galaxy.datatypes.data import Text
from galaxy.datatypes.tabular import Tabular
from galaxy.datatypes.sequence import Fasta
from galaxy import util
from galaxy.datatypes.images import Html


log = logging.getLogger(__name__)

        finally:
            fh.close()
        return False


## Qiime Classes

class QiimeMetadataMapping(Tabular):
    MetadataElement( name="column_names", default=[], desc="Column Names", readonly=False, visible=True, no_value=[] )
    file_ext = 'qiimemapping'

26:5c77423823cb

from galaxy.datatypes.data import Text
from galaxy.datatypes.tabular import Tabular
from galaxy.datatypes.sequence import Fasta
from galaxy import util
from galaxy.datatypes.images import Html
import pkg_resources
pkg_resources.require("simplejson")
import simplejson


log = logging.getLogger(__name__)

        finally:
            fh.close()
        return False


## Biom 

class BiologicalObservationMatrix( Text ):
    file_ext = 'biom'
    """
    http://biom-format.org/documentation/biom_format.html
    The format of the file is JSON:
    {
    "id":null,
    "format": "Biological Observation Matrix 0.9.1-dev",
    "format_url": "http://biom-format.org",
    "type": "OTU table",
    "generated_by": "QIIME revision 1.4.0-dev",
    "date": "2011-12-19T19:00:00",
    "rows":[
            {"id":"GG_OTU_1", "metadata":null},
            {"id":"GG_OTU_2", "metadata":null},
            {"id":"GG_OTU_3", "metadata":null},
        ],
    "columns": [
            {"id":"Sample1", "metadata":null},
            {"id":"Sample2", "metadata":null}
        ],
    "matrix_type": "sparse",
    "matrix_element_type": "int",
    "shape": [3, 2],
    "data":[[0,1,1],
            [1,0,5],
            [2,1,4]
           ]
    }

    """

    def __init__(self, **kwd):
        Text.__init__( self, **kwd )

    def sniff( self, filename ):
        if os.path.getsize(filename) < 50000:
            try:
                data = simplejson.load(open(filename))
                if data['format'].find('Biological Observation Matrix'):
                    return True
            except:
                pass
        return False




## Qiime Classes

class QiimeMetadataMapping(Tabular):
    MetadataElement( name="column_names", default=[], desc="Column Names", readonly=False, visible=True, no_value=[] )
    file_ext = 'qiimemapping'