From 7f69c48a6a4e47df54d2fdc7a7e8c8b5ab86a822 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Mon, 1 Nov 2010 17:16:03 -0700 Subject: [PATCH] Two lines between functions (trivial change) --- extra/ucsc_encode_submission/ucsc_gather.py | 36 +++++++++++++++++---- 1 file changed, 29 insertions(+), 7 deletions(-) diff --git a/extra/ucsc_encode_submission/ucsc_gather.py b/extra/ucsc_encode_submission/ucsc_gather.py index 191281c..5487cfd 100755 --- a/extra/ucsc_encode_submission/ucsc_gather.py +++ b/extra/ucsc_encode_submission/ucsc_gather.py @@ -15,7 +15,6 @@ import urllib import urllib2 import urlparse - from htsworkflow.util import api from htsworkflow.pipelines.sequences import \ create_sequence_table, \ @@ -30,8 +29,7 @@ def main(cmdline=None): elif opts.verbose: logging.basicConfig(level = logging.INFO ) else: - logging.basicConfig(level = logging.WARNING ) - + logging.basicConfig(level = logging.WARNING ) apidata = {'apiid': opts.apiid, 'apikey': opts.apikey } @@ -61,6 +59,7 @@ def main(cmdline=None): if opts.makeddf: make_all_ddfs(library_result_map, opts.daf) + def make_parser(): # Load defaults from the config files config = SafeConfigParser() @@ -110,6 +109,7 @@ def make_parser(): return parser + def build_fastqs(host, apidata, sequences_path, library_result_map, force=False ): """ @@ -182,6 +182,7 @@ environment="PYTHONPATH=/home/diane/lib/python2.6/site-packages:/home/diane/proj qseq_condor_header, qseq_condor_entries) + def find_missing_targets(library_result_map, lib_db, force=False): """ Check if the sequence file exists. @@ -233,6 +234,7 @@ def find_missing_targets(library_result_map, lib_db, force=False): return needed_targets + def link_daf(daf_path, library_result_map): if not os.path.exists(daf_path): raise RuntimeError("%s does not exist, how can I link to it?" % (daf_path,)) @@ -244,6 +246,7 @@ def link_daf(daf_path, library_result_map): if not os.path.exists(submission_daf): os.link(daf_path, submission_daf) + def make_submission_ini(host, apidata, library_result_map, paired=True): # ma is "map algorithm" ma = 'TH1014' @@ -355,6 +358,7 @@ def make_submission_ini(host, apidata, library_result_map, paired=True): f = open(result_ini,'w') f.write(os.linesep.join(inifile)) + def make_lane_dict(lib_db, lib_id): """ Convert the lane_set in a lib_db to a dictionary @@ -365,6 +369,7 @@ def make_lane_dict(lib_db, lib_id): result.append((lane['flowcell'], lane)) return dict(result) + def make_all_ddfs(library_result_map, daf_name, make_condor=True): dag_fragment = [] for lib_id, result_dir in library_result_map: @@ -419,6 +424,7 @@ def make_ddf(ininame, daf_name, guess_ddf=False, make_condor=False, outdir=None return dag_fragments + def read_ddf_ini(filename, output=sys.stdout): """ Read a ini file and dump out a tab delmited text file @@ -447,7 +453,8 @@ def read_ddf_ini(filename, output=sys.stdout): 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. @@ -465,7 +472,8 @@ def read_library_result_map(filename): library_id, result_dir = line.split() results.append((library_id, result_dir)) return results - + + def make_condor_archive_script(ininame, files): script = """Universe = vanilla @@ -493,6 +501,7 @@ queue condor_stream.close() return condor_script + def make_condor_upload_script(ininame): script = """Universe = vanilla @@ -515,6 +524,7 @@ queue condor_stream.close() return condor_script + def make_dag_fragment(ininame, archive_condor, upload_condor): """ Make the couple of fragments compress and then upload the data. @@ -531,11 +541,13 @@ def make_dag_fragment(ininame, archive_condor, upload_condor): return fragments + def get_library_info(host, apidata, library_id): url = api.library_url(host, library_id) contents = api.retrieve_info(url, apidata) return contents + def condor_srf_to_fastq(srf_file, target_pathname, paired, flowcell=None, mid=None, force=False): args = [ srf_file, ] @@ -569,6 +581,7 @@ queue return script + def condor_qseq_to_fastq(qseq_file, target_pathname, flowcell=None, force=False): args = ['-i', qseq_file, '-o', target_pathname ] if flowcell is not None: @@ -619,6 +632,7 @@ def find_archive_sequence_files(host, apidata, sequences_path, return lib_db + def find_best_extension(extension_map, filename): """ Search through extension_map looking for the best extension @@ -638,7 +652,8 @@ def find_best_extension(extension_map, filename): elif len(ext) > len(best_ext): best_ext = ext return best_ext - + + def make_submission_section(line_counter, files, standard_attributes, file_attributes): """ Create a section in the submission ini file @@ -653,19 +668,23 @@ def make_submission_section(line_counter, files, standard_attributes, file_attri inifile += ["%s=%s" % (k,v)] return inifile + def make_base_name(pathname): base = os.path.basename(pathname) name, ext = os.path.splitext(base) return name + def make_submission_name(ininame): name = make_base_name(ininame) return name + '.tgz' + def make_ddf_name(pathname): name = make_base_name(pathname) return name + '.ddf' + def make_condor_name(pathname, run_type=None): name = make_base_name(pathname) elements = [name] @@ -673,6 +692,7 @@ def make_condor_name(pathname, run_type=None): elements.append(run_type) elements.append('condor') return ".".join(elements) + def make_submit_script(target, header, body_list): """ @@ -703,6 +723,7 @@ def make_submit_script(target, header, body_list): def parse_filelist(file_string): return file_string.split(',') + def validate_filelist(files): """ Die if a file doesn't exist in a file list @@ -710,6 +731,7 @@ def validate_filelist(files): for f in files: if not os.path.exists(f): raise RuntimeError("%s does not exist" % (f,)) - + + if __name__ == "__main__": main() -- 2.30.2