def out_put(self): TEMPLATE = '{workdir}/face_tracking/{corpus}/{show}.txt' video = self.in_video().task corpus = video.corpus show = video.show path = TEMPLATE.format(workdir=self.workdir, corpus=corpus, show=show) return sciluigi.TargetInfo(self, path)
def out_bed(self): basename1 = os.path.splitext(os.path.basename( self.in_regions().path))[0] return sciluigi.TargetInfo( self, os.path.join(self.outdir, '%s.random_%.0e.bed' % (basename1, self.num_random)))
def out_rnafold(self, ): basename = os.path.splitext(os.path.basename(self.in_fasta().path))[0] if self.constraint: outfile = os.path.join(self.outdir, basename + '.constraint.dG.dat' ) else: outfile = os.path.join(self.outdir, basename + '.dG.dat' ) return sciluigi.TargetInfo(self, outfile)
def out_file(self): return sciluigi.TargetInfo( self, os.path.join( self.outdir, os.path.splitext(os.path.basename(self.in_filename().path))[0] + '_muts.dat'))
def out_bed(self): basename1 = os.path.splitext(os.path.basename( self.in_regions().path))[0] basename2 = os.path.splitext(os.path.basename(self.motif))[0] return sciluigi.TargetInfo( self, os.path.join(self.outdir, '%s.%s.bed' % (basename1, basename2)))
def out_data(self, ): filenames = [target().path for target in self.in_data.values()] return sciluigi.TargetInfo( self, os.path.join( self.outdir, processing.combine_filenames_split(filenames) + '.combined_data.gz'))
def out_table(self, ): filenames = [target().path for target in self.in_counts.values()] return sciluigi.TargetInfo( self, os.path.join( self.outdir, processing.combine_filenames_split(filenames) + '.temp%d.combined_data.gz' % self.temperature))
def out_bed(self): basenames = processing.combine_filenames( [target().path for target in self.in_beds]) basename = '.'.join(basenames) return sciluigi.TargetInfo( self, os.path.join(self.outdir, basename + '.bed'))
def out_fastq2(self): path = self._output_from_hash() target = sl.TargetInfo( self, os.path.join(os.path.dirname(path), os.path.basename(self.in_fastq2().path))) target.target.makedirs() return target
def out_table(self, ): filenames = [ os.path.basename(subdict.values()[0]().path) for windowsize, subdict in self.in_secstructure.items() ] #filenames = [os.path.basename(target().path) for target in self.in_secstructure.values()] filename = processing.combine_filenames_split( filenames, avoid_elements=['dat', 'constraint']) return sciluigi.TargetInfo( self, os.path.join(self.outdir, filename + '.combined_data.gz'))
class Foo2Bar(sl.Task): ''' Another dummy task ''' replacement = luigi.Parameter() in_foo = sl.TargetInfo(None, 'None') def out_bar(self): return sl.TargetInfo( self, self.in_foo().path + '.{r}.txt'.format(r=self.replacement)) def run(self): self.ex('sed "s/foo/{r}/g" {inf} > {outf}'.format( r=self.replacement, inf=self.in_foo().path, outf=self.out_bar().path))
def out_put(self): INA_TEMPLATE = '{corpus_dir}/INA/LAffaireSnowden/medias_reencoded/tv/{show}.mp4' UPC_TEMPLATE = '{corpus_dir}/3-24/media/{show}.mp4' DW_TEMPLATE = '{corpus_dir}/DW/{show}.mp4' TRAILER_TEMPLATE = '{corpus_dir}/{show}.mp4' TVD_TEMPLATE = '{corpus_dir}/{corpus}/dvd/rip/video/{show}.mkv' EASTENDERS_TEMPLATE = '{corpus_dir}/{show}.mp4' if self.corpus == 'INA': path = INA_TEMPLATE.format(corpus_dir=self.corpus_dir, show=self.show) elif self.corpus == 'UPC': path = UPC_TEMPLATE.format(corpus_dir=self.corpus_dir, show=self.show) elif self.corpus == 'DW': path = DW_TEMPLATE.format(corpus_dir=self.corpus_dir, show=self.show) elif self.corpus == 'TRAILER': path = TRAILER_TEMPLATE.format(corpus_dir=self.corpus_dir, show=self.show) elif self.corpus == 'TheBigBangTheory': path = TVD_TEMPLATE.format(corpus=self.corpus, corpus_dir=self.corpus_dir, show=self.show) elif self.corpus == 'GameOfThrones': path = TVD_TEMPLATE.format(corpus=self.corpus, corpus_dir=self.corpus_dir, show=self.show) elif self.corpus == 'EastEnders': path = EASTENDERS_TEMPLATE.format(corpus_dir=self.corpus_dir, show=self.show) else: raise NotImplementedError('') return sciluigi.TargetInfo(self, path)
def out_put(self): INA_TEMPLATE = '{corpus_dir}/INA/LAffaireSnowden/medias_reencoded/tv/{show}.wav' UPC_TEMPLATE = '{corpus_dir}/3-24/{show}.wav' # DW_TEMPLATE = '{corpus_dir}/DW/{show}.wav' if self.corpus == 'INA': path = INA_TEMPLATE.format(corpus_dir=self.corpus_dir, show=self.show) elif self.corpus == 'UPC': path = UPC_TEMPLATE.format(corpus_dir=self.corpus_dir, show=self.show) elif self.corpus == 'DW': raise NotImplementedError('') else: raise NotImplementedError('') return sciluigi.TargetInfo(self, path)
def out_trimmo(self): outp_name = 'trimmed_seq' adapter_full_path = self.adapters_path + self.adapter self.default_trimmo_args = OrderedDict() args = [ 'SE', 'PE', '-basein', '-baseout', 'ILLUMINACLIP:', 'MAXINFO:', 'SLIDINGWINDOW:', 'LEADING:', 'CROP:', 'TRAILING:', 'HEADCROP:', 'MINLEN:' ] vals = [ None, True, None, None, adapter_full_path + ':2:30:10', None, None, 30, None, 30, 15, 20 ] # "leading": head_qual, "trailing": 30, "headcrop": 15} for arg, vals in zip_longest(args, vals): self.default_trimmo_args[arg] = vals # TODO move this constants to config file # print(self.default_trimmo_args) # print(self.tool_path) print(self.outp_path + 'trimmo_res.txt') return sl.TargetInfo(self, self.outp_path + 'trimmo_res.txt')
def out_report(self): outf_path = 'data/' + self.run_id + '/testrun_dataset_liblinear_datareport.csv' return sl.TargetInfo( self, outf_path ) # We manually re-create the filename that this should have
def out_replatot(self): return sl.TargetInfo(self, self.in_data().path + '.atot')
def out_rawdata(self): return sl.TargetInfo(self, 'data/acgt.txt')
def out_multi(self): return [ sl.TargetInfo(self, itgt.path + '.daa.txt') for itgt in self.in_multi() ]
def out_done(self): return sl.TargetInfo(self, self.in_lowestrmsd().path + '.mainwf_done')
def out_merged(self): return sl.TargetInfo(self, self.in_data1().path + '.merged.txt')
def out_data1(self): return sl.TargetInfo(self, 'data/' + self.text + '.txt')
def out_put(self): TEMPLATE = '{workdir}/external/gregory/lists/{episode}.txt' path = TEMPLATE.format( workdir=self.workdir, episode=pyannote_workflows.tasks.tvd_dataset.get_episode(self)) return sciluigi.TargetInfo(self, path)
def out_sequences(self): return sciluigi.TargetInfo( self, os.path.join(self.outdir, 'library_%s' % self.lib_name + '.dat'))
def out_file(self): return sciluigi.TargetInfo(self, self.filename)
def out_put(self): TEMPLATE = '{workdir}/_models/dlib.face.landmarks.dat' path = TEMPLATE.format(workdir=self.workdir) return sciluigi.TargetInfo(self, path)
def out_fastq(self): return [ sl.TargetInfo(self, fastqc_res) for fastqc_res in glob.glob(self.outp_path + '*') ]
def out_put(self): TEMPLATE = '{workdir}/_models/openface.nn4.small2.v1.t7' path = TEMPLATE.format(workdir=self.workdir) return sciluigi.TargetInfo(self, path)
def out_trimmo(self): return [ sl.TargetInfo(self, trimmo_res) for trimmo_res in glob.glob(self.outp_path + '*') ]
def out_data(self): return sl.TargetInfo(self, self.outp_path)
def out_multi(self): return [ sl.TargetInfo(self, '/tmp/out_%s_%d.txt' % (self.an_id, i)) for i in xrange(10) ]