comparison mothur/lib/galaxy/datatypes/metagenomics.py @ 27:49058b1f8d3f

Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur

26:5c77423823cb

for Mothur
"""

import logging, os, os.path, sys, time, tempfile, shutil, string, glob, re
import galaxy.model
from galaxy.datatypes import data
from galaxy.datatypes.sniff import *
from galaxy.datatypes import metadata
from galaxy.datatypes import tabular
from galaxy.datatypes import sequence
from galaxy.datatypes.metadata import MetadataElement
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__)


## Mothur Classes 

class Otu( Text ):
    file_ext = 'otu'

            pass
        finally:
            close(fh)
        return False

class RefTaxonomy(Tabular):
    file_ext = 'ref.taxonomy'
    """
        A table with 2 or 3 columns:
        - SequenceName

        2	0	2	2	Root;Bacteria;Bacteroidetes
    """
    MetadataElement( name="column_names", default=[], desc="Column Names", readonly=False, visible=True, no_value=[] )
    file_ext = 'qiimeotutable'
    def init_meta( self, dataset, copy_from=None ):
        tabular.Tabular.init_meta( self, dataset, copy_from=copy_from )
    def set_meta( self, dataset, overwrite = True, skip = None, **kwd ):
        self.set_column_names(dataset) 
    def set_column_names(self, dataset):
        if dataset.has_data():
            dataset_fh = open( dataset.file_name )

        PC.355	3.177	0.0	3.444
        PC.356	1.955	3.444	0.0
    """
    file_ext = 'qiimedistmat'
    def init_meta( self, dataset, copy_from=None ):
        tabular.Tabular.init_meta( self, dataset, copy_from=copy_from )
    def set_meta( self, dataset, overwrite = True, skip = None, **kwd ):
        self.set_column_names(dataset) 
    def set_column_names(self, dataset):
        if dataset.has_data():
            dataset_fh = open( dataset.file_name )

27:49058b1f8d3f

for Mothur
"""

import logging, os, os.path, sys, time, tempfile, shutil, string, glob, re
import galaxy.model
from galaxy.datatypes.sniff import *
from galaxy.datatypes.metadata import MetadataElement
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__)

## Mothur Classes 

class Otu( Text ):
    file_ext = 'otu'

            pass
        finally:
            close(fh)
        return False

class CountTable(Tabular):
    MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] )
    file_ext = 'count_table'

    def __init__(self, **kwd):
        """
        A table with first column names and following columns integer counts
        # Example 1:
        Representative_Sequence total   
        U68630  1
        U68595  1
        U68600  1
        # Example 2 (with group columns):
        Representative_Sequence total   forest  pasture 
        U68630  1       1       0       
        U68595  1       1       0       
        U68600  1       1       0       
        U68591  1       1       0       
        U68647  1       0       1       
        """
        Tabular.__init__( self, **kwd )
        self.column_names = ['name','total']

    def set_meta( self, dataset, overwrite = True, skip = 1, max_data_lines = None, **kwd ):
        try:
            data_lines = 0;
            fh = open( dataset.file_name )
            line = fh.readline()
            if line:
                line = line.strip()
                colnames = line.split() 
                if len(colnames) > 1:
                    dataset.metadata.columns = len( colnames )
                    if len(colnames) > 2:
                        dataset.metadata.groups = colnames[2:]
                    column_types = ['str']
                    for i in range(1,len(colnames)):
                        column_types.append('int')
                    dataset.metadata.column_types = column_types
                    dataset.metadata.comment_lines = 1
            while line:
                line = fh.readline()
                if not line: break
                data_lines += 1
            dataset.metadata.data_lines = data_lines
        finally:
            close(fh)

class RefTaxonomy(Tabular):
    file_ext = 'ref.taxonomy'
    """
        A table with 2 or 3 columns:
        - SequenceName

        2	0	2	2	Root;Bacteria;Bacteroidetes
    """
    MetadataElement( name="column_names", default=[], desc="Column Names", readonly=False, visible=True, no_value=[] )
    file_ext = 'qiimeotutable'
    def init_meta( self, dataset, copy_from=None ):
        Tabular.init_meta( self, dataset, copy_from=copy_from )
    def set_meta( self, dataset, overwrite = True, skip = None, **kwd ):
        self.set_column_names(dataset) 
    def set_column_names(self, dataset):
        if dataset.has_data():
            dataset_fh = open( dataset.file_name )

        PC.355	3.177	0.0	3.444
        PC.356	1.955	3.444	0.0
    """
    file_ext = 'qiimedistmat'
    def init_meta( self, dataset, copy_from=None ):
        Tabular.init_meta( self, dataset, copy_from=copy_from )
    def set_meta( self, dataset, overwrite = True, skip = None, **kwd ):
        self.set_column_names(dataset) 
    def set_column_names(self, dataset):
        if dataset.has_data():
            dataset_fh = open( dataset.file_name )