annotate lib/galaxy/datatypes/snpeff.py @ 0:e8adfc4c0a6b draft

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"""
SnpEff datatypes
"""
import os,os.path,re,sys
import galaxy.datatypes.data
from galaxy.datatypes.data import Text
from galaxy.datatypes.metadata import MetadataElement

class SnpEffDb( Text ):
    """Class describing an IGV tiled data file (TDF) .tdf  binary file"""
    file_ext = "snpeffdb"
    MetadataElement( name="genome_version", default=None, desc="Genome Version", readonly=True, visible=True, no_value=None )
    MetadataElement( name="regulation", default=[], desc="Regulation Names", readonly=True, visible=True, no_value=[] )
    MetadataElement( name="annotation", default=[], desc="Annotation Names", readonly=True, visible=True, no_value=[] )

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

    def set_meta( self, dataset, **kwd ):
        Text.set_meta(self, dataset, **kwd )
        data_dir = dataset.extra_files_path
        ## search data_dir/genome_version for files
        regulation_pattern = 'regulation_(.+).bin'
        #  annotation files that are included in snpEff by a flag
        annotations_dict = {'nextProt.bin' : '-nextprot','motif.bin': '-motif'}
        regulations = []
        annotations = []
        if data_dir and os.path.isdir(data_dir):
            for root, dirs, files in os.walk(data_dir):
                for fname in files:
                    if fname.startswith('snpEffectPredictor'):
                        # if snpEffectPredictor.bin download succeeded
                        genome_version = os.path.basename(root)
                        dataset.metadata.genome_version = genome_version
                    else:
                        m = re.match(regulation_pattern,fname)
                        if m:
                            name = m.groups()[0]
                            regulations.append(name)
                        elif fname in annotations_dict:
                            value = annotations_dict[fname]
                            name = value.lstrip('-')
                            annotations.append(name)
            dataset.metadata.regulation = regulations
            dataset.metadata.annotation = annotations