def create_gtf_annotation(logger,ws_client,hs_client,internal_services,ws_id,genome_ref,genome_id,fasta_file,directory,token):
try:
tmp_file = os.path.join(directory,genome_id + "_GFF.gff")
fasta_file= generate_fasta(logger,internal_services,token,genome_ref,directory,genome_id)
logger.info("Sanitizing the fasta file to correct id names {}".format(datetime.datetime.utcnow()))
mapping_filename = c_mapping.create_sanitized_contig_ids(fasta_file)
c_mapping.replace_fasta_contig_ids(fasta_file, mapping_filename, to_modified=True)
logger.info("Generating FASTA file completed successfully : {}".format(datetime.datetime.utcnow()))
generate_gff(logger,internal_services,token,genome_ref,directory,genome_id,tmp_file)
c_mapping.replace_gff_contig_ids(tmp_file, mapping_filename, to_modified=True)
gtf_path = os.path.join(directory,genome_id+"_GTF.gtf")
gtf_cmd = " -E {0} -T -o {1}".format(tmp_file,gtf_path)
try:
logger.info("Executing: gffread {0}".format(gtf_cmd))
cmdline_output = runProgram(None,"gffread",gtf_cmd,None,directory)
except Exception as e:
raise Exception("Error Converting the GFF file to GTF using gffread {0},{1}".format(gtf_cmd,"".join(traceback.format_exc())))
#if os.path.exists(tmp_file): os.remove(tmp_file)
if os.path.exists(gtf_path):
annotation_handle = hs_client.upload(gtf_path)
a_handle = { "handle" : annotation_handle ,"size" : os.path.getsize(gtf_path), 'genome_id' : genome_ref}
##Saving GFF/GTF annotation to the workspace
res= ws_client.save_objects(
{"workspace":ws_id,
"objects": [{
"type":"KBaseRNASeq.GFFAnnotation",
"data":a_handle,
"name":genome_id+"_GTF_Annotation",
"hidden":1}
]})
except Exception as e:
raise ValueError("Generating GTF file from Genome Annotation object Failed : {}".format("".join(traceback.format_exc())))
return gtf_path
reads)
missing_objs = [i for i in reads if not i in e_ws_objs]
if len(e_ws_objs) != len(reads):
raise Exception(
'Missing Library objects {0} in the {1}. please copy them and run this method'
.format(",".join(missing_objs), params['ws_id']))
### Build Hisat2 index
fasta_file = script_util.generate_fasta(logger, services, token,
annotation_id, hisat2_dir,
params['genome_id'])
logger.info("Sanitizing the fasta file to correct id names {}".format(
datetime.datetime.utcnow()))
mapping_filename = c_mapping.create_sanitized_contig_ids(fasta_file)
c_mapping.replace_fasta_contig_ids(fasta_file,
mapping_filename,
to_modified=True)
logger.info("Generating FASTA file completed successfully : {}".format(
datetime.datetime.utcnow()))
hisat2base = os.path.join(
hisat2_dir, handler_util.get_file_with_suffix(hisat2_dir, ".fasta"))
hisat2base_cmd = '{0} {1}'.format(fasta_file, hisat2base)
try:
logger.info("Building Index for Hisat2 {0}".format(hisat2base_cmd))
cmdline_output = script_util.runProgram(logger, "hisat2-build",
hisat2base_cmd, None,
hisat2_dir)
except Exception, e:
raise Exception("Failed to run command {0}".format(hisat2base_cmd))
ws_gtf = params['genome_id'] + "_GTF"
ret = script_util.if_obj_exists(None, ws_client, params['ws_id'],
logger.info("GFF Annotation Exist for Genome Annotation {0}.... Skipping step ".format(annotation_name))
gtf_obj= ws_client.get_objects([{'name' : gtf_obj_name,'workspace' : params['ws_id']}])[0]
gtf_info = ws_client.get_object_info_new({"objects": [{'name': gtf_obj_name, 'workspace': params['ws_id']}]})[0]
gtf_annotation_id = str(gtf_info[6]) + '/' + str(gtf_info[0]) + '/' + str(gtf_info[4])
gtf_id=gtf_obj['data']['handle']['id']
gtf_name=gtf_obj['data']['handle']['file_name']
try:
script_util.download_file_from_shock(logger, shock_service_url=services['shock_service_url'], shock_id=gtf_id,filename=gtf_name, directory=diffexp_dir,token=token)
gtf_file = os.path.join(diffexp_dir,gtf_name)
except Exception,e:
raise Exception( "Unable to download shock file, {0}".format(gtf_name))
else:
fasta_file= script_util.generate_fasta(logger,services,token,annotation_id,diffexp_dir,annotation_name)
logger.info("Sanitizing the fasta file to correct id names {}".format(datetime.datetime.utcnow()))
mapping_filename = c_mapping.create_sanitized_contig_ids(fasta_file)
c_mapping.replace_fasta_contig_ids(fasta_file, mapping_filename, to_modified=True)
logger.info("Generating FASTA file completed successfully : {}".format(datetime.datetime.utcnow()))
gtf_file = script_util.create_gtf_annotation(logger,ws_client,hs,services,params['ws_id'],annotation_id,gtf_obj_name,fasta_file,diffexp_dir,token)
m_expr_ids = e_sample['data']['mapped_expression_ids']
m_align_exp = []
labels = []
expressions = []
counter = 0
assembly_file = os.path.join(diffexp_dir,ASSEMBLY_GTF_FN)
list_file = open(assembly_file,'w')
for i in m_expr_ids:
for a_id ,e_id in i.items():
#print a_id + ":" + e_id
files = {}
a_obj,e_obj = ws_client.get_objects(
[{'ref' : a_id},{'ref': e_id}])
