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Merge pull request #22 from databio/dev_newplots
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| Original file line number | Diff line number | Diff line change |
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@@ -3,7 +3,7 @@ | |
| bedfile statistics generating pipeline | ||
| """ | ||
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| __author__ = ["Michal Stolarczyk", "Ognen Duzlevski"] | ||
| __author__ = ["Michal Stolarczyk", "Ognen Duzlevski", "Jose Verdezoto"] | ||
| __email__ = "[email protected]" | ||
| __version__ = "0.0.1" | ||
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@@ -12,41 +12,64 @@ | |
| import json | ||
| import yaml | ||
| import os | ||
| import warnings | ||
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| import pypiper | ||
| from bbconf.const import * | ||
| import pypiper | ||
| import bbconf | ||
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| parser = ArgumentParser(description="A pipeline to read a file in BED format and produce metadata in JSON format.") | ||
| parser = ArgumentParser( | ||
| description="A pipeline to read a file in BED format and produce metadata " | ||
| "in JSON format.") | ||
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| parser.add_argument('--bedfile', help='a full path to bed file to process', required=True) | ||
| parser.add_argument("--bedbase-config", dest="bedbase_config", type=str, required=False, default=None, | ||
| help="a path to the bedbase configuratiion file") | ||
| parser.add_argument("-y", "--sample-yaml", dest="sample_yaml", type=str, required=False, | ||
| help="a yaml config file with sample attributes to pass on more metadata into the database") | ||
| parser.add_argument( | ||
| '--bedfile', help='a full path to bed file to process', required=True) | ||
| parser.add_argument( | ||
| '--open-signal-matrix', type=str, required=False, default=None, | ||
| help='a full path to the openSignalMatrix required for the tissue ' | ||
| 'specificity plots') | ||
| parser.add_argument( | ||
| "--bedbase-config", dest="bedbase_config", type=str, default=None, | ||
| help="a path to the bedbase configuratiion file") | ||
| parser.add_argument( | ||
| "-y", "--sample-yaml", dest="sample_yaml", type=str, required=False, | ||
| help="a yaml config file with sample attributes to pass on more metadata " | ||
| "into the database") | ||
| exclusive_group = parser.add_mutually_exclusive_group() | ||
| exclusive_group.add_argument('--no-db-commit', action='store_true', | ||
| help='whether the JSON commit to the database should be skipped') | ||
| exclusive_group.add_argument('--just-db-commit', action='store_true', | ||
| help='whether just to commit the JSON to the database') | ||
| parser = pypiper.add_pypiper_args(parser, groups=["pypiper", "common", "looper", "ngs"]) | ||
| exclusive_group.add_argument( | ||
| '--no-db-commit', action='store_true', | ||
| help='whether the JSON commit to the database should be skipped') | ||
| exclusive_group.add_argument( | ||
| '--just-db-commit', action='store_true', | ||
| help='whether just to commit the JSON to the database') | ||
| parser = pypiper.add_pypiper_args(parser, | ||
| groups=["pypiper", "common", "looper", "ngs"]) | ||
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| args = parser.parse_args() | ||
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| bbc = bbconf.BedBaseConf(filepath=bbconf.get_bedbase_cfg(args.bedbase_config)) | ||
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| bed_digest = md5(open(args.bedfile, 'rb').read()).hexdigest() | ||
| bedfile_name = os.path.split(args.bedfile)[1] | ||
| fileid = os.path.splitext(os.path.splitext(bedfile_name)[0])[0] # twice since there are 2 exts | ||
| outfolder = os.path.abspath(os.path.join(bbc[CFG_PATH_KEY][CFG_BEDSTAT_OUTPUT_KEY], bed_digest)) | ||
| # need to split twice since there are 2 exts | ||
| fileid = os.path.splitext(os.path.splitext(bedfile_name)[0])[0] | ||
| outfolder = os.path.abspath(os.path.join( | ||
| bbc[CFG_PATH_KEY][CFG_BEDSTAT_OUTPUT_KEY], bed_digest)) | ||
| json_file_path = os.path.abspath(os.path.join(outfolder, fileid + ".json")) | ||
|
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| if not args.just_db_commit: | ||
| pm = pypiper.PipelineManager(name="bedstat-pipeline", outfolder=outfolder, args=args) | ||
| rscript_path = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "tools", "regionstat.R") | ||
| assert os.path.exists(rscript_path), FileNotFoundError("'{}' script not found".format(rscript_path)) | ||
| cmd_vars = dict(rscript=rscript_path, bed=args.bedfile, id=fileid, out=outfolder, genome=args.genome_assembly, digest=bed_digest) | ||
| command = "Rscript {rscript} --bedfile={bed} --fileId={id} --outputfolder={out} --genome={genome} --digest={digest}".format(**cmd_vars) | ||
| pm = pypiper.PipelineManager(name="bedstat-pipeline", outfolder=outfolder, | ||
| args=args) | ||
| rscript_path = os.path.join(os.path.dirname( | ||
| os.path.dirname(os.path.abspath(__file__))), "tools", "regionstat.R") | ||
| assert os.path.exists(rscript_path), \ | ||
| FileNotFoundError("'{}' script not found".format(rscript_path)) | ||
| cmd_vars = dict(rscript=rscript_path, bed=args.bedfile, id=fileid, | ||
| matrix=args.open_signal_matrix, out=outfolder, | ||
| genome=args.genome_assembly, digest=bed_digest) | ||
| command = "Rscript {rscript} --bedfile={bed} --fileId={id} " \ | ||
| "--openSignalMatrix={matrix} --outputfolder={out} " \ | ||
| "--genome={genome} --digest={digest}".format(**cmd_vars) | ||
| pm.run(cmd=command, target=json_file_path) | ||
| pm.stop_pipeline() | ||
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@@ -68,13 +91,15 @@ | |
| except KeyError: | ||
| print("'{}' metadata not available".format(key)) | ||
| else: | ||
| warnings.warn("Specified sample_yaml path does not exist: {}".format(args.sample_yaml)) | ||
| warnings.warn("Specified sample_yaml path does not exist: {}". | ||
| format(args.sample_yaml)) | ||
| # enrich the data from R with the data from the sample line itself | ||
| # the bedfile_path below needs to be overwritten in Elastic in case the pipeline run was split | ||
| # into two computing environments. Currently used for the development. | ||
| # This concept leverages the potability introduced by environment variable in the | ||
| # bedfile path in the PEP. Locally the environment variable points to a different path than on | ||
| # the compute cluster where the heavy calculations happen. | ||
| # the bedfile_path below needs to be overwritten in Elastic in case the | ||
| # pipeline run was split into two computing environments. Currently used | ||
| # for the development. This concept leverages the potability introduced by | ||
| # environment variable in the bedfile path in the PEP. Locally the | ||
| # environment variable points to a different path than on the compute | ||
| # cluster where the heavy calculations happen. | ||
| data[BEDFILE_PATH_KEY] = [args.bedfile] | ||
| print("Data: {}".format(data)) | ||
| bbc.insert_bedfiles_data(data=data, doc_id=bed_digest) | ||
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,13 +1,11 @@ | ||
| protocol_mapping: | ||
| bedstat: bedstat | ||
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| pipelines: | ||
| bedstat: | ||
| name: BEDSTAT | ||
| path: pipeline/bedstat.py | ||
| schema: pep_schema.yaml | ||
| looper_args: True | ||
| command_template: > | ||
| { pipeline.path } | ||
| --bedfile { sample.output_file_path } | ||
| --genome { sample.genome } | ||
| pipeline_name: BEDSTAT | ||
| pipeline_type: sample | ||
| path: pipeline/bedstat.py | ||
| input_schema: http://schema.databio.org/pipelines/bedstat.yaml | ||
| command_template: > | ||
| {pipeline.path} | ||
| --bedfile {sample.output_file_path} | ||
| --genome {sample.genome} | ||
| --sample-yaml {sample.yaml_file} | ||
| {% if sample.bedbase_config is defined %} --bedbase-config {sample.bedbase_config} {% endif %} | ||
| {% if sample.open_signal_matrix is defined %} --open-signal-matrix {sample.open_signal_matrix} {% endif %} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| pep_version: 2.0.0 | ||
| sample_table: path | ||
| looper: | ||
| output_dir: output | ||
| sample_modifiers: | ||
| append: | ||
| pipeline_interfaces: ../pipeline_interface_new.yaml |
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