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()