""" # load modules from ruffus import * import CGATCore.Experiment as E import sys import os import glob import sqlite3 from CGATCore import Pipeline as P import CGATPipelines.PipelineTracks as PipelineTracks # load options from the config file P.getParameters([ "%s/pipeline.ini" % __file__[:-len(".py")], "../pipeline.ini", "pipeline.ini" ]) PARAMS = P.PARAMS PARAMS_ANNOTATIONS = P.peekParameters(PARAMS["annotations_dir"], "pipeline_annotations.py") Sample = PipelineTracks.Sample TRACKS = PipelineTracks.Tracks(Sample).loadFromDirectory( glob.glob("medip_*"), "medip_(\S+)") def connect(): '''connect to database.
import os import glob import sqlite3 import CGATCore.IOTools as IOTools from CGATCore import Pipeline as P import CGATPipelines.PipelineTracks as PipelineTracks ################################################### ################################################### ################################################### # Pipeline configuration ################################################### # load options from the config file P.getParameters( ["%s/pipeline.ini" % os.path.splitext(__file__)[0], "../pipeline.ini", "pipeline.ini"]) PARAMS = P.PARAMS PARAMS_ANNOTATIONS = P.peekParameters(PARAMS["annotations_dir"], "pipeline_annotations.py") ################################################################### ################################################################### # Helper functions mapping tracks to conditions, etc ################################################################### TRACKS = PipelineTracks.Tracks(PipelineTracks.Sample).loadFromDirectory( glob.glob("*.fastq.gz"), "(\S+).fastq.gz") USECLUSTER = True
import CGATCore.Experiment as E from CGATCore import Pipeline as P import CGATCore.IOTools as IOTools import CGAT.IndexedFasta as IndexedFasta ################################################### ################################################### ################################################### # Pipeline configuration ################################################### # load options from the config file P.getParameters([ "%s/pipeline.ini" % os.path.splitext(__file__)[0], "../pipeline.ini", "pipeline.ini" ], defaults={"maps": ""}) PARAMS = P.PARAMS ################################################################### ################################################################### ################################################################### ## ################################################################### if os.path.exists("pipeline_conf.py"): L.info("reading additional configuration from pipeline_conf.py") exec(compile(open("pipeline_conf.py").read(), "pipeline_conf.py", 'exec')) PARAMS = P.getParameters()
print(INI_file) elif (f_count > 1 or f_count == 0): print('You have no project configuration (".yml") file or more than one', 'in the directory:', '\n', path) sys.exit(''' Exiting. You will have to manually edit the Sphinx conf.py file. ''') return(INI_file) modulename = 'P' if modulename in sys.modules: ini_file = 'pipelin{}.yml'.format(r'(.*)') P.getParameters( ["{}/{}".format(os.path.splitext(__file__)[0], ini_file), "../{}".format(ini_file), "{}".format(ini_file), ], ) PARAMS = P.PARAMS else: # Get location to this file: here = os.path.abspath(os.path.dirname(__file__)) ini_file = getINIdir(os.path.abspath(here)) # Print keys (sections): if not os.path.exists(ini_file): sys.exit('''Something isn't right with the paths. The yml/ini file does not seem to exist...''') else:
import CGATCore.Experiment as E from CGATCore import Pipeline as P import CGAT.GTF as GTF import CGATCore.IOTools as IOTools import CGATPipelines.PipelineLncRNA as PipelineLncRNA ################################################### # Pipeline configuration ################################################### P.getParameters( [ "%s/pipeline.ini" % os.path.splitext(__file__)[0], "../pipeline.ini", "pipeline.ini" ], defaults={ "annotations_dir": "", "genesets_abinitio_coding": "pruned.gtf.gz", "genesets_abinitio_lncrna": "pruned.gtf.gz", "genesets_reference": "reference.gtf.gz", "genesets_refcoding": "refcoding.gtf.gz", "genesets_previous": "" }) PARAMS = P.PARAMS PARAMS.update( P.peekParameters(PARAMS["annotations_annotations_dir"], "pipeline_annotations.py", prefix="annotations_", update_interface=True))
import CGAT.GTF as GTF import CGATCore.IOTools as IOTools ################################################### ################################################### ################################################### # Pipeline configuration ################################################### # load options from the config file from CGATCore import Pipeline as P from functools import reduce P.getParameters( ["%s/pipeline.ini" % os.path.splitext(__file__)[0], "../pipeline.ini", "pipeline.ini"], defaults={ 'annotations_dir': "", 'paired_end': False}) PARAMS = P.PARAMS PARAMS_ANNOTATIONS = P.peekParameters( PARAMS["annotations_dir"], "pipeline_annotations.py") # get options that are to be tested cufflinks_options = {} if "cufflinks_test_options" in PARAMS: options = P.asList(PARAMS["cufflinks_test_options"]) for option in options:
if os.path.exists("conf.py"): exec(compile(open("conf.py").read(), "conf.py", 'exec')) TARGET_ANNOTATION = 'ensembl_regions.gff' TARGET_GENESET = 'ensembl.gtf' TARGET_PROMOTORS = 'promotors.gtf' TARGET_TSS = 'tss.gtf' TARGET_REPEATS = 'repeats.gff' TARGET_TRANSCRIPTS = 'transcripts.gtf.gz' TARGET_PROBESET = 'probeset.gtf' TARGET_TRANSCRIPTS_TSS = 'transcripts_tss.gtf' TARGET_TRANSCRIPTS_PROMOTORS = 'transcripts_promotors.gtf' TARGET_ANNOTATOR_GENETERRITORIES = 'annotator_geneterritories.gff' TARGET_MAPPABILITY = 'mappability.bed' PARAMS = P.getParameters() @files(((None, "probeset2gene.table"), )) def buildProbeset2Gene(infile, outfile): '''build map relating a probeset to an ENSEMBL gene_id''' Expression.buildProbeset2Gene(infile, outfile) @follows(buildProbeset2Gene) def prepare(): pass @files([((x, "%s.map" % x), "%s_levels.import" % x[:-len("_series_matrix.txt.gz")])
import CGATCore.Experiment as E import logging as L import CGATPipelines.PipelineUCSC as PipelineUCSC from ruffus import * ################################################### ################################################### ################################################### # Pipeline configuration ################################################### from CGATCore import Pipeline as P P.getParameters([ "%s/pipeline.ini" % os.path.splitext(__file__)[0], "../pipeline.ini", "pipeline.ini" ], defaults={ 'query': "", 'target': "" }) PARAMS = P.PARAMS if os.path.exists("pipeline_conf.py"): L.info("reading additional configuration from pipeline_conf.py") exec(compile(open("pipeline_conf.py").read(), "pipeline_conf.py", 'exec')) def getGenomes(): '''return genome names of query and target.''' genome_query = os.path.join(PARAMS["genome_dir"], PARAMS["query"]) genome_target = os.path.join(PARAMS["genome_dir"], PARAMS["target"])
import sys import glob import os import itertools import sqlite3 import CGATCore.Experiment as E from CGATCore import Pipeline as P import PipelineGeneset as PGeneset ################################################################### ################################################################### ################################################################### # read global options from configuration file P.getParameters([ "%s/pipeline.ini" % os.path.splitext(__file__)[0], "../pipeline.ini", "pipeline.ini" ], defaults={'polyphen_modes': ""}) P.PARAMS.update({ "transcripts": "transcripts.gtf.gz", "genes": 'genes.gtf.gz', "annotation": 'geneset_regions.gff.gz', "peptides": 'peptides.fasta', "cdna": 'cdna.fasta', "cds": 'cds.fasta' }) PARAMS = P.PARAMS PGeneset.PARAMS = PARAMS
import sqlite3 import io import fileinput import CGAT.Fastq as fq import logging as L import CGATCore.Experiment as E import CGATPipelines.PipelineMapping as PipelineMapping from ruffus import * ################################################################### ################################################################### ################################################################### # Pipeline configuration from CGATCore import Pipeline as P P.getParameters(["pipeline.ini"]) PARAMS = P.PARAMS USECLUSTER = True ################################################################### ################################################################### ################################################################### # Count raw reads @transform("*.fastq.1.gz", regex(r"(\S+).fastq.1.gz"), r"\1.nreads") def countReads(infile, outfile): '''count number of reads in input files.''' to_cluster = True m = PipelineMapping.Counter() statement = m.build((infile,), outfile)
'pipeline_docs', 'themes') logopath = os.path.join(themedir, "cgat_logo.png") ################################################################ # Import pipeline configuration from pipeline.ini in the current # directory and the common one. # PATH were code for pipelines is stored pipelinesdir = os.path.dirname(CGATPipelines.__file__) # The default configuration file - 'inifile' is read by # sphinx-report. inifile = os.path.join(os.path.dirname(CGATPipelines.__file__), 'configuration', 'pipeline.ini') PARAMS = P.getParameters([inifile, "pipeline.ini"]) def setup(app): app.add_config_value('PARAMS', {}, True) ################################################################ ################################################################ ################################################################ # The pipeline assumes that sphinxreport is called within the # working directory. If the report is in a separate build directory, # change the paths below. # # directory with export directory from pipeline # This should be a directory in the build directory - you can
Code ==== """ from ruffus import * import sys import os import sqlite3 from CGATCore import Experiment as E from CGATCore import Pipeline as P import re # load options from the config file PARAMS = P.getParameters([ "%s/pipeline.yml" % os.path.splitext(__file__)[0], "../pipeline.yml", "pipeline.yml" ]) PARAMS["projectsrc"] = os.path.dirname(__file__) #for key, value in PARAMS.iteritems(): # print "%s:\t%s" % (key,value) # add configuration values from associated pipelines # # 1. pipeline_annotations: any parameters will be added with the # prefix "annotations_". The interface will be updated with # "annotations_dir" to point to the absolute path names. PARAMS.update( P.peekParameters(PARAMS["annotations_dir"], "pipeline_annotations.py", on_error_raise=__name__ == "__main__",