import urlparse
from htsworkflow.util import api
+from htsworkflow.util.rdfhelp import \
+ dafTermOntology, \
+ fromTypedNode, \
+ get_model, \
+ get_serializer, \
+ load_into_model, \
+ submissionOntology
+from htsworkflow.submission.daf import DAFMapper, get_submission_uri
from htsworkflow.submission.condorfastq import CondorFastqExtract
+logger = logging.getLogger('ucsc_gather')
+
def main(cmdline=None):
parser = make_parser()
opts, args = parser.parse_args(cmdline)
apidata = api.make_auth_from_opts(opts, parser)
+ model = get_model(opts.load_model)
+ mapper = DAFMapper(opts.name, opts.daf, model)
+ submission_uri = get_submission_uri(opts.name)
+ if opts.load_rdf is not None:
+ load_into_model(model, 'turtle', opts.load_rdf, submission_uri)
+
if opts.makeddf and opts.daf is None:
parser.error("Please specify your daf when making ddf files")
if opts.make_tree_from is not None:
make_tree_from(opts.make_tree_from, library_result_map)
- if opts.daf is not None:
- link_daf(opts.daf, library_result_map)
+ #if opts.daf is not None:
+ # link_daf(opts.daf, library_result_map)
if opts.fastq:
extractor = CondorFastqExtract(opts.host, apidata, opts.sequence,
force=opts.force)
extractor.build_fastqs(library_result_map)
- if opts.ini:
- make_submission_ini(opts.host, apidata, library_result_map)
+ if opts.scan_submission:
+ scan_submission_dirs(mapper, library_result_map)
if opts.makeddf:
- make_all_ddfs(library_result_map, opts.daf, force=opts.force)
+ make_all_ddfs(mapper, library_result_map, force=opts.force)
+ if opts.print_rdf:
+ writer = get_serializer()
+ print writer.serialize_model_to_string(model)
+
def make_parser():
parser = OptionParser()
+ parser.add_option('--name', help="Set submission name")
+ parser.add_option('--load-model', default=None,
+ help="Load model database")
+ parser.add_option('--load-rdf', default=None,
+ help="load rdf statements into model")
+ parser.add_option('--print-rdf', action="store_true", default=False,
+ help="print ending model state")
+
# commands
parser.add_option('--make-tree-from',
help="create directories & link data files",
parser.add_option('--fastq', help="generate scripts for making fastq files",
default=False, action="store_true")
- parser.add_option('--ini', help="generate submission ini file", default=False,
- action="store_true")
-
+ parser.add_option('--scan-submission', default=False, action="store_true",
+ help="Import metadata for submission into our model")
+
parser.add_option('--makeddf', help='make the ddfs', default=False,
action="store_true")
return parser
-
def make_tree_from(source_path, library_result_map):
"""Create a tree using data files from source path.
"""
os.link(daf_path, submission_daf)
-def make_submission_ini(host, apidata, library_result_map, paired=True):
- #attributes = get_filename_attribute_map(paired)
- view_map = NameToViewMap(host, apidata)
-
- candidate_fastq_src = {}
-
+def scan_submission_dirs(view_map, library_result_map):
+ """Look through our submission directories and collect needed information
+ """
for lib_id, result_dir in library_result_map:
- order_by = ['order_by=files', 'view', 'replicate', 'cell',
- 'readType', 'mapAlgorithm', 'insertLength', 'md5sum' ]
- inifile = ['[config]']
- inifile += [" ".join(order_by)]
- inifile += ['']
- line_counter = 1
- result_ini = os.path.join(result_dir, result_dir+'.ini')
-
- # write other lines
- submission_files = os.listdir(result_dir)
- fastqs = {}
- fastq_attributes = {}
- for f in submission_files:
- attributes = view_map.find_attributes(f, lib_id)
- if attributes is None:
- raise ValueError("Unrecognized file: %s" % (f,))
- attributes['md5sum'] = "None"
-
- ext = attributes["extension"]
- if attributes['view'] is None:
- continue
- elif attributes.get("type", None) == 'fastq':
- fastqs.setdefault(ext, set()).add(f)
- fastq_attributes[ext] = attributes
- else:
- md5sum = make_md5sum(os.path.join(result_dir,f))
- if md5sum is not None:
- attributes['md5sum']=md5sum
- inifile.extend(
- make_submission_section(line_counter,
- [f],
- attributes
- )
- )
- inifile += ['']
- line_counter += 1
- # add in fastqs on a single line.
-
- for extension, fastq_files in fastqs.items():
- inifile.extend(
- make_submission_section(line_counter,
- fastq_files,
- fastq_attributes[extension])
- )
- inifile += ['']
- line_counter += 1
-
- f = open(result_ini,'w')
- f.write(os.linesep.join(inifile))
-
+ view_map.import_submission_dir(result_dir, lib_id)
-def make_all_ddfs(library_result_map, daf_name, make_condor=True, force=False):
+def make_all_ddfs(view_map, library_result_map, make_condor=True, force=False):
dag_fragment = []
for lib_id, result_dir in library_result_map:
- ininame = result_dir+'.ini'
- inipathname = os.path.join(result_dir, ininame)
- if os.path.exists(inipathname):
- dag_fragment.extend(
- make_ddf(ininame, daf_name, True, make_condor, result_dir)
- )
+ submissionNode = view_map.get_submission_node(result_dir)
+ dag_fragment.extend(
+ make_ddf(view_map, submissionNode, make_condor, result_dir)
+ )
if make_condor and len(dag_fragment) > 0:
dag_filename = 'submission.dagman'
f.close()
-def make_ddf(ininame, daf_name, guess_ddf=False, make_condor=False, outdir=None):
+def make_ddf(view_map, submissionNode, make_condor=False, outdir=None):
"""
Make ddf files, and bonus condor file
"""
if outdir is not None:
os.chdir(outdir)
output = sys.stdout
- ddf_name = None
- if guess_ddf:
- ddf_name = make_ddf_name(ininame)
- print ddf_name
- output = open(ddf_name,'w')
-
- file_list = read_ddf_ini(ininame, output)
- logging.info(
- "Read config {0}, found files: {1}".format(
- ininame, ", ".join(file_list)))
- file_list.append(daf_name)
- if ddf_name is not None:
- file_list.append(ddf_name)
+ name = fromTypedNode(view_map.model.get_target(submissionNode, submissionOntology['name']))
+ if name is None:
+ logging.error("Need name for %s" % (str(submissionNode)))
+ return []
+
+ ddf_name = name + '.ddf'
+ output = sys.stdout
+ # output = open(ddf_name,'w')
- if make_condor:
- archive_condor = make_condor_archive_script(ininame, file_list)
- upload_condor = make_condor_upload_script(ininame)
-
- dag_fragments.extend(
- make_dag_fragment(ininame, archive_condor, upload_condor)
- )
+ # filename goes first
+ variables = ['filename']
+ variables.extend(view_map.get_daf_variables())
+ output.write('\t'.join(variables))
+ output.write(os.linesep)
+
+ submission_views = view_map.model.get_targets(submissionNode, submissionOntology['has_view'])
+ file_list = []
+ for viewNode in submission_views:
+ record = []
+ for variable_name in variables:
+ varNode = dafTermOntology[variable_name]
+ values = [fromTypedNode(v) for v in list(view_map.model.get_targets(viewNode, varNode))]
+ if variable_name == 'filename':
+ file_list.extend(values)
+ if len(values) == 0:
+ attribute = "#None#"
+ elif len(values) == 1:
+ attribute = values[0]
+ else:
+ attribute = ",".join(values)
+ record.append(attribute)
+ output.write('\t'.join(record))
+ output.write(os.linesep)
+
+ logging.info(
+ "Examined {0}, found files: {1}".format(
+ str(submissionNode), ", ".join(file_list)))
+
+ #file_list.append(daf_name)
+ #if ddf_name is not None:
+ # file_list.append(ddf_name)
+ #
+ #if make_condor:
+ # archive_condor = make_condor_archive_script(ininame, file_list)
+ # upload_condor = make_condor_upload_script(ininame)
+ #
+ # dag_fragments.extend(
+ # make_dag_fragment(ininame, archive_condor, upload_condor)
+ # )
os.chdir(curdir)
return dag_fragments
-def read_ddf_ini(filename, output=sys.stdout):
- """
- Read a ini file and dump out a tab delmited text file
- """
- file_list = []
- config = SafeConfigParser()
- config.read(filename)
-
- order_by = shlex.split(config.get("config", "order_by"))
-
- output.write("\t".join(order_by))
- output.write(os.linesep)
- sections = config.sections()
- sections.sort()
- for section in sections:
- if section == "config":
- # skip the config block
- continue
- values = []
- for key in order_by:
- v = config.get(section, key)
- values.append(v)
- if key == 'files':
- file_list.extend(parse_filelist(v))
-
- output.write("\t".join(values))
- output.write(os.linesep)
- return file_list
-
-
def read_library_result_map(filename):
"""
Read a file that maps library id to result directory.
return contents
-class NameToViewMap(object):
- """Determine view attributes for a given submission file name
- """
- def __init__(self, root_url, apidata):
- self.root_url = root_url
- self.apidata = apidata
-
- self.lib_cache = {}
- self.lib_paired = {}
- # ma is "map algorithm"
- ma = 'TH1014'
-
- self.patterns = [
- # for 2011 Feb 18 elements submission
- ('final_Cufflinks_genes_*gtf', 'GeneDeNovo'),
- ('final_Cufflinks_transcripts_*gtf', 'TranscriptDeNovo'),
- ('final_exonFPKM-Cufflinks-0.9.3-GENCODE-v3c-*.gtf',
- 'ExonsGencV3c'),
- ('final_GENCODE-v3-Cufflinks-0.9.3.genes-*gtf',
- 'GeneGencV3c'),
- ('final_GENCODE-v3-Cufflinks-0.9.3.transcripts-*gtf',
- 'TranscriptGencV3c'),
- ('final_TSS-Cufflinks-0.9.3-GENCODE-v3c-*.gtf', 'TSS'),
- ('final_junctions-*.bed6+3', 'Junctions'),
-
- ('*.bai', None),
- ('*.splices.bam', 'Splices'),
- ('*.bam', self._guess_bam_view),
- ('junctions.bed', 'Junctions'),
- ('*.jnct', 'Junctions'),
- ('*unique.bigwig', None),
- ('*plus.bigwig', 'PlusSignal'),
- ('*minus.bigwig', 'MinusSignal'),
- ('*.bigwig', 'Signal'),
- ('*.tar.bz2', None),
- ('*.condor', None),
- ('*.daf', None),
- ('*.ddf', None),
-
- ('*ufflinks?0.9.3.genes.gtf', 'GeneDeNovo'),
- ('*ufflinks?0.9.3.transcripts.gtf', 'TranscriptDeNovo'),
- ('*GENCODE-v3c.exonFPKM.gtf', 'ExonsGencV3c'),
- ('*GENCODE-v3c.genes.gtf', 'GeneGencV3c'),
- ('*GENCODE-v3c.transcripts.gtf', 'TranscriptGencV3c'),
- ('*GENCODE-v3c.TSS.gtf', 'TSS'),
- ('*.junctions.bed6+3', 'Junctions'),
-
- ('*.?ufflinks-0.9.0?genes.expr', 'GeneDeNovo'),
- ('*.?ufflinks-0.9.0?transcripts.expr', 'TranscriptDeNovo'),
- ('*.?ufflinks-0.9.0?transcripts.gtf', 'GeneModel'),
-
- ('*.GENCODE-v3c?genes.expr', 'GeneGCV3c'),
- ('*.GENCODE-v3c?transcript*.expr', 'TranscriptGCV3c'),
- ('*.GENCODE-v3c?transcript*.gtf', 'TranscriptGencV3c'),
- ('*.GENCODE-v4?genes.expr', None), #'GeneGCV4'),
- ('*.GENCODE-v4?transcript*.expr', None), #'TranscriptGCV4'),
- ('*.GENCODE-v4?transcript*.gtf', None), #'TranscriptGencV4'),
- ('*_1.75mers.fastq', 'FastqRd1'),
- ('*_2.75mers.fastq', 'FastqRd2'),
- ('*_r1.fastq', 'FastqRd1'),
- ('*_r2.fastq', 'FastqRd2'),
- ('*.fastq', 'Fastq'),
- ('*.gtf', 'GeneModel'),
- ('*.ini', None),
- ('*.log', None),
- ('*.md5', None),
- ('paired-end-distribution*', 'InsLength'),
- ('*.stats.txt', 'InsLength'),
- ('*.srf', None),
- ('*.wig', None),
- ('*.zip', None),
- ('transfer_log', None),
- ]
-
- self.views = {
- None: {"MapAlgorithm": "NA"},
- "Paired": {"MapAlgorithm": ma},
- "Aligns": {"MapAlgorithm": ma},
- "Single": {"MapAlgorithm": ma},
- "Splices": {"MapAlgorithm": ma},
- "Junctions": {"MapAlgorithm": ma},
- "PlusSignal": {"MapAlgorithm": ma},
- "MinusSignal": {"MapAlgorithm": ma},
- "Signal": {"MapAlgorithm": ma},
- "GeneModel": {"MapAlgorithm": ma},
- "GeneDeNovo": {"MapAlgorithm": ma},
- "TranscriptDeNovo": {"MapAlgorithm": ma},
- "ExonsGencV3c": {"MapAlgorithm": ma},
- "GeneGencV3c": {"MapAlgorithm": ma},
- "TSS": {"MapAlgorithm": ma},
- "GeneGCV3c": {"MapAlgorithm": ma},
- "TranscriptGCV3c": {"MapAlgorithm": ma},
- "TranscriptGencV3c": {"MapAlgorithm": ma},
- "GeneGCV4": {"MapAlgorithm": ma},
- "TranscriptGCV4": {"MapAlgorithm": ma},
- "FastqRd1": {"MapAlgorithm": "NA", "type": "fastq"},
- "FastqRd2": {"MapAlgorithm": "NA", "type": "fastq"},
- "Fastq": {"MapAlgorithm": "NA", "type": "fastq" },
- "InsLength": {"MapAlgorithm": ma},
- }
- # view name is one of the attributes
- for v in self.views.keys():
- self.views[v]['view'] = v
-
- def find_attributes(self, pathname, lib_id):
- """Looking for the best extension
- The 'best' is the longest match
-
- :Args:
- filename (str): the filename whose extention we are about to examine
- """
- path, filename = os.path.splitext(pathname)
- if not self.lib_cache.has_key(lib_id):
- self.lib_cache[lib_id] = get_library_info(self.root_url,
- self.apidata, lib_id)
-
- lib_info = self.lib_cache[lib_id]
- if lib_info['cell_line'].lower() == 'unknown':
- logging.warn("Library %s missing cell_line" % (lib_id,))
- attributes = {
- 'cell': lib_info['cell_line'],
- 'replicate': lib_info['replicate'],
- }
- is_paired = self._is_paired(lib_id, lib_info)
-
- if is_paired:
- attributes.update(self.get_paired_attributes(lib_info))
- else:
- attributes.update(self.get_single_attributes(lib_info))
-
- for pattern, view in self.patterns:
- if fnmatch.fnmatch(pathname, pattern):
- if callable(view):
- view = view(is_paired=is_paired)
-
- attributes.update(self.views[view])
- attributes["extension"] = pattern
- return attributes
-
-
- def _guess_bam_view(self, is_paired=True):
- """Guess a view name based on library attributes
- """
- if is_paired:
- return "Paired"
- else:
- return "Aligns"
-
-
- def _is_paired(self, lib_id, lib_info):
- """Determine if a library is paired end"""
- # TODO: encode this information in the library type page.
- single = (1,3,6)
- if len(lib_info["lane_set"]) == 0:
- # we haven't sequenced anything so guess based on library type
- if lib_info['library_type_id'] in single:
- return False
- else:
- return True
-
- if not self.lib_paired.has_key(lib_id):
- is_paired = 0
- isnot_paired = 0
- failed = 0
- # check to see if all the flowcells are the same.
- # otherwise we might need to do something complicated
- for flowcell in lib_info["lane_set"]:
- # yes there's also a status code, but this comparison
- # is easier to read
- if flowcell["status"].lower() == "failed":
- # ignore failed flowcell
- failed += 1
- pass
- elif flowcell["paired_end"]:
- is_paired += 1
- else:
- isnot_paired += 1
-
- logging.debug("Library %s: %d paired, %d single, %d failed" % \
- (lib_info["library_id"], is_paired, isnot_paired, failed))
-
- if is_paired > isnot_paired:
- self.lib_paired[lib_id] = True
- elif is_paired < isnot_paired:
- self.lib_paired[lib_id] = False
- else:
- raise RuntimeError("Equal number of paired & unpaired lanes."\
- "Can't guess library paired status")
-
- return self.lib_paired[lib_id]
-
- def get_paired_attributes(self, lib_info):
- if lib_info['insert_size'] is None:
- errmsg = "Library %s is missing insert_size, assuming 200"
- logging.warn(errmsg % (lib_info["library_id"],))
- insert_size = 200
- else:
- insert_size = lib_info['insert_size']
- return {'insertLength': insert_size,
- 'readType': '2x75'}
-
- def get_single_attributes(self, lib_info):
- return {'insertLength':'ilNA',
- 'readType': '1x75D'
- }
-
def make_submission_section(line_counter, files, attributes):
"""
Create a section in the submission ini file
projects / htsworkflow.git / blobdiff