PARAMS = P.PARAMS ################################################################### ################################################################### ## Helper functions mapping tracks to conditions, etc ################################################################### import CGATPipelines.PipelineTracks as PipelineTracks # collect fastq.gz tracks TRACKS = PipelineTracks.Tracks( PipelineTracks.Sample3 ).loadFromDirectory( glob.glob( "*.fastq.gz" ), "(\S+).fastq.gz" ) +\ PipelineTracks.Tracks( PipelineTracks.Sample3 ).loadFromDirectory( glob.glob( "*.fastq.1.gz" ), "(\S+).fastq.1.gz" ) ALL = PipelineTracks.Sample3() EXPERIMENTS = PipelineTracks.Aggregate(TRACKS, labels=("condition", "tissue")) CONDITIONS = PipelineTracks.Aggregate(TRACKS, labels=("condition", )) TISSUES = PipelineTracks.Aggregate(TRACKS, labels=("tissue", )) ################################################################### ## Global flags ################################################################### ASSEMBLERS = P.asList(PARAMS["general_assemblers"]) METAGENOME = "meta-velvet" in ASSEMBLERS or "ibda" in ASSEMBLERS or "cortex_var" in ASSEMBLERS ASSEMBLERS = P.asList(PARAMS["assemblers"]) MAPPER = PARAMS["coverage_mapper"] BOWTIE = MAPPER == "bowtie" BWA = MAPPER == "bwa"
"pipeline_annotations.py") PipelineiCLIP.PARAMS = PARAMS PipelineiCLIP.PARAMS_ANNOTATIONS = PARAMS_ANNOTATIONS PARAMS["project_src"] = os.path.join(os.path.dirname(__file__), "..") ################################################################### # Helper functions mapping tracks to conditions, etc ################################################################### import CGATPipelines.PipelineTracks as PipelineTracks # define some tracks if needed TRACKS = PipelineTracks.Tracks(PipelineTracks.Sample3) for line in IOTools.openFile("sample_table.tsv"): track = line.split("\t")[2] TRACKS.tracks.append(PipelineTracks.Sample3(filename=track)) ################################################################### def connect(): '''connect to database. Use this method to connect to additional databases. Returns a database connection. ''' dbh = sqlite3.connect(PARAMS["database"]) statement = '''ATTACH DATABASE '%s' as annotations''' \ % (PARAMS["annotations_database"]) cc = dbh.cursor()