comparison blast.py @ 9:2bda64d39931 draft

Uploaded v0.0.19, adds blastdbp and pssm-asn1 datatypes.

8:de11e1a921c4

"""
BlastXml class
"""

from galaxy.datatypes.data import get_file_peek
from galaxy.datatypes.data import Text, Data
from galaxy.datatypes.xml import GenericXml
from galaxy.datatypes.metadata import MetadataElement

from time import sleep
import os

                                     to_ext, size, offset, **kwd)
        if self.file_ext == "blastdbn":
            title = "This is a nucleotide BLAST database"
        elif self.file_ext =="blastdbp":
            title = "This is a protein BLAST database"
        else:
            #Error?                                                                                                                                                                     
            title = "This is a BLAST database."
        msg = ""
        try:
            #Try to use any text recorded in the dummy index file:
            handle = open(data.file_name, "rU")

        self.add_composite_file('blastdb.psi', is_binary=True, optional=True)
#        self.add_composite_file('blastdb.paa', is_binary=True, optional=True)
#        self.add_composite_file('blastdb.pab', is_binary=True, optional=True)
#        self.add_composite_file('blastdb.pac', is_binary=True, optional=True)
# The last 3 lines should be repeated for each WriteDB column, with filename extensions like ('.pba', '.pbb', '.pbc'), ('.pca', '.pcb', '.pcc'), etc.

9:2bda64d39931

"""
BlastXml class
"""

from galaxy.datatypes.data import get_file_peek
from galaxy.datatypes.data import Text, Data, GenericAsn1
from galaxy.datatypes.xml import GenericXml
from galaxy.datatypes.metadata import MetadataElement

from time import sleep
import os

                                     to_ext, size, offset, **kwd)
        if self.file_ext == "blastdbn":
            title = "This is a nucleotide BLAST database"
        elif self.file_ext =="blastdbp":
            title = "This is a protein BLAST database"
        elif self.file_ext =="blastdbd":
            title = "This is a domain BLAST database"
        else:
            #Error?
            title = "This is a BLAST database."
        msg = ""
        try:
            #Try to use any text recorded in the dummy index file:
            handle = open(data.file_name, "rU")

        self.add_composite_file('blastdb.psi', is_binary=True, optional=True)
#        self.add_composite_file('blastdb.paa', is_binary=True, optional=True)
#        self.add_composite_file('blastdb.pab', is_binary=True, optional=True)
#        self.add_composite_file('blastdb.pac', is_binary=True, optional=True)
# The last 3 lines should be repeated for each WriteDB column, with filename extensions like ('.pba', '.pbb', '.pbc'), ('.pca', '.pcb', '.pcc'), etc.


class BlastDomainDb( _BlastDb, Data ):
    """Class for domain BLAST database files."""
    file_ext = 'blastdbd'
    allow_datatype_change = False
    composite_type = 'basic'

    def __init__(self, **kwd):
        Data.__init__(self, **kwd)
        self.add_composite_file('blastdb.phr', is_binary=True)
        self.add_composite_file('blastdb.pin', is_binary=True)
        self.add_composite_file('blastdb.psq', is_binary=True)
        self.add_composite_file('blastdb.freq', is_binary=True, optional=True)
        self.add_composite_file('blastdb.loo', is_binary=True, optional=True)
        self.add_composite_file('blastdb.psd', is_binary=True, optional=True)
        self.add_composite_file('blastdb.psi', is_binary=True, optional=True)
        self.add_composite_file('blastdb.rps', is_binary=True, optional=True)
        self.add_composite_file('blastdb.aux', is_binary=True, optional=True)