annotate rsem.py @ 1:e5082fcdc0bd default tip

correct Tabular path

"""
RSEM datatypes
"""
import os,os.path,re,sys
from galaxy.datatypes.data import get_file_peek
from galaxy.datatypes.images import Html
from galaxy.datatypes.tabular import Tabular
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.sniff import get_headers

import logging

log = logging.getLogger(__name__)

class RsemIsoformsResults( Tabular ):
    file_ext = "rsem.isoforms.results"
    """
    required columns:
    transcript_id gene_id length effective_length expected_count TPM FPKM IsoPct 
    optional columns:
    pme_expected_count pme_TPM pme_FPKM IsoPct_from_pme_TPM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound
    """
    def __init__(self, **kwd):
        Tabular.__init__( self, **kwd )
        """Initialize RsemResults datatype"""
        self.comment_lines = 1
    def sniff( self, filename ):
        headers = get_headers( filename, '\n', count=1 )
        return len(headers) > 0 and len(headers[0]) >= 8 and headers[0][0] == "transcript_id" and headers[0][1] == "gene_id" and headers[0][6] == "FPKM"
    def set_meta( self, dataset, **kwd ):
        Tabular.set_meta( self, dataset, skip=None, **kwd )

class RsemGenesResults( Tabular ):
    file_ext = "rsem.genes.results"
    """
    required columns:
    gene_id transcript_id(s) length effective_length expected_count TPM FPKM
    optional columns:
    pme_expected_count pme_TPM pme_FPKM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound
    """
    def __init__(self, **kwd):
        Tabular.__init__( self, **kwd )
        """Initialize RsemResults datatype"""
        self.comment_lines = 1
    def sniff( self, filename ):
        headers = get_headers( filename, '\n', count=1 )
        return len(headers) > 0 and len(headers[0]) >= 7 and headers[0][0] == "gene_id" and headers[0][1].startswith("transcript_id") and headers[0][6] == "FPKM"
    def set_meta( self, dataset, **kwd ):
        Tabular.set_meta( self, dataset, skip=None, **kwd )

class RsemReference( Html ):
    """Class describing an RSEM reference"""
    MetadataElement( name='reference_name', default='rsem_ref' , desc='RSEM Reference Name', readonly=True, visible=True, set_in_upload=True, no_value='rsem_ref' )
    file_ext = 'rsem_ref'
    allow_datatype_change = False
    composite_type = 'auto_primary_file'
    def __init__( self, **kwd ):
        Html.__init__(self, **kwd)
        """
        Expecting files:
        extra_files_path/<reference_name>.grp
        extra_files_path/<reference_name>.ti
        extra_files_path/<reference_name>.seq
        extra_files_path/<reference_name>.transcripts.fa
        Optionally includes files:
        extra_files_path/<reference_name>.chrlist
        extra_files_path/<reference_name>.idx.fa
        extra_files_path/<reference_name>.1.ebwt
        extra_files_path/<reference_name>.2.ebwt
        extra_files_path/<reference_name>.3.ebwt
        extra_files_path/<reference_name>.4.ebwt
        extra_files_path/<reference_name>.rev.1.ebwt
        extra_files_path/<reference_name>.rev.2.ebwt
        """
        self.add_composite_file( '%s.grp', description = 'Group File', substitute_name_with_metadata = 'reference_name', is_binary = False )
        self.add_composite_file( '%s.ti', description = '', substitute_name_with_metadata = 'reference_name', is_binary = False )
        self.add_composite_file( '%s.seq', description = '', substitute_name_with_metadata = 'reference_name', is_binary = False )
        self.add_composite_file( '%s.transcripts.fa', description = '', substitute_name_with_metadata = 'reference_name', is_binary = False )
        self.add_composite_file( '%s.chrlist', description = '', substitute_name_with_metadata = 'reference_name', is_binary = False, optional=True )
        self.add_composite_file( '%s.idx.fa', description = '', substitute_name_with_metadata = 'reference_name', is_binary = False, optional=True )
        self.add_composite_file( '%s.1.ebwt', description = '', substitute_name_with_metadata = 'reference_name', is_binary = True, optional=True )
        self.add_composite_file( '%s.2.ebwt', description = '', substitute_name_with_metadata = 'reference_name', is_binary = True, optional=True )
        self.add_composite_file( '%s.3.ebwt', description = '', substitute_name_with_metadata = 'reference_name', is_binary = True, optional=True )
        self.add_composite_file( '%s.4.ebwt', description = '', substitute_name_with_metadata = 'reference_name', is_binary = True, optional=True )
        self.add_composite_file( '%s.rev.1.ebwt', description = '', substitute_name_with_metadata = 'reference_name', is_binary = True, optional=True )
        self.add_composite_file( '%s.rev.2.ebwt', description = '', substitute_name_with_metadata = 'reference_name', is_binary = True, optional=True )

    def generate_primary_file( self, dataset = None ):
        """ 
        This is called only at upload to write the file
        cannot rename the datasets here - they come with the default unfortunately
        """

    def regenerate_primary_file(self,dataset):
        """
        cannot do this until we are setting metadata 
        """
        link_to_exts = ['.grp','.ti','.seq','.fa','.chrlist','.log']
        ref_name = dataset.metadata.reference_name
        efp = dataset.extra_files_path
        flist = os.listdir(efp)
        rval = ['<html><head><title>%s</title></head><body><p/>RSEM Reference   %s   files:<p/><ul>' % (dataset.name,ref_name)]
        rvalb = []
        for i,fname in enumerate(flist):
            sfname = os.path.split(fname)[-1]
            f,e = os.path.splitext(fname)
            if e in link_to_exts:
                rval.append( '<li><a href="%s">%s</a></li>' % ( sfname, sfname) )
            else:
                rvalb.append( '<li>%s</li>' % (sfname) )
        if len(rvalb) > 0:
            rval += rvalb
        rval.append( '</ul></body></html>' )
        fh = file(dataset.file_name,'w')
        fh.write("\n".join( rval ))
        fh.write('\n')
        fh.close()

    def set_meta( self, dataset, **kwd ):
        Html.set_meta( self, dataset, **kwd )
        efp = dataset.extra_files_path
        flist = os.listdir(efp)
        for i,fname in enumerate(flist):
            if fname.endswith('.grp'):
                dataset.metadata.reference_name = fname[:-4]
                break
        self.regenerate_primary_file(dataset)