Mercurial > repos > jjohnson > rsem_datatypes

changeset 0:77151afcd323

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jjohnson
date Mon, 10 Mar 2014 08:09:01 -0400
parents
children e5082fcdc0bd
files datatypes_conf.xml rsem.py
diffstat 2 files changed, 142 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Mon Mar 10 08:09:01 2014 -0400
@@ -0,0 +1,14 @@
+<?xml version="1.0"?>
+<datatypes>
+    <datatype_files>
+        <datatype_file name="rsem.py"/>
+    </datatype_files>
+    <registration>
+        <datatype extension="rsem_ref" type="galaxy.datatypes.rsem:RsemReference" display_in_upload="true"/>
+        <datatype extension="rsem.genes.results" type="galaxy.datatypes.rsem:RsemGenesResults" display_in_upload="true"/>
+        <datatype extension="rsem.isoforms.results" type="galaxy.datatypes.rsem:RsemIsoformsResults" display_in_upload="true"/>
+        <datatype extension="rsem.ngvec" type="galaxy.datatypes.data:Tabular" subclass="True" display_in_upload="true"/>
+        <datatype extension="rsem.genemat" type="galaxy.datatypes.data:Tabular" subclass="True" display_in_upload="true"/>
+        <datatype extension="rsem.isomat" type="galaxy.datatypes.data:Tabular" subclass="True" display_in_upload="true"/>
+    </registration>
+</datatypes>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rsem.py	Mon Mar 10 08:09:01 2014 -0400
@@ -0,0 +1,128 @@
+"""
+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)
+