예제 #1
0
                    alignment.align(referenceName,
                                    readsFile,
                                    bidirectional=False,
                                    mark_duplicates=False,
                                    realign=False,
                                    skip_sorting=True,
                                    aligner_opts_extra="",
                                    logfile=os.path.join(
                                        RECALIBRATION_RESULTS,
                                        "alignmentQC_out.txt"),
                                    output_dir=RECALIBRATION_RESULTS,
                                    output_basename="samplelib")

                    # Generate both hpTable and hpModel.
                    flow_space_recal.calibrate(RECALIBRATION_RESULTS,
                                               sample_map_path,
                                               env['recalibArgs'], chipflow)

                # merge step, calibrate collects the training data saved for each barcode,
                # calculate and generate hpTable and hpModel files for the whole dataset
                flow_space_recal.HPaggregation(
                    os.path.join(env['BASECALLER_RESULTS'], "recalibration"),
                    env['recalibArgs'])

                hptable = os.path.join(env['BASECALLER_RESULTS'],
                                       "recalibration", "hpTable.txt")
                printtime("hptable: %s" % hptable)

                additional_basecallerArgs = " --calibration-file " + hptable
                additional_basecallerArgs += " --phase-estimation-file " + os.path.join(
                    env['BASECALLER_RESULTS'], "recalibration",
예제 #2
0
파일: BlockTLScript.py 프로젝트: rb94/TS
                    alignment.align(
                        referenceName,
                        readsFile,
                        bidirectional=False,
                        mark_duplicates=False,
                        realign=False,
                        skip_sorting=True,
                        aligner_opts_extra="",
                        logfile=os.path.join(RECALIBRATION_RESULTS,"alignmentQC_out.txt"),
                        output_dir=RECALIBRATION_RESULTS,
                        output_basename="samplelib")

                    # Generate both hpTable and hpModel.
                    flow_space_recal.calibrate(
                        RECALIBRATION_RESULTS,
                        sample_map_path,
                        env['recalibArgs'],
                        chipflow)

                # merge step, calibrate collects the training data saved for each barcode,
                # calculate and generate hpTable and hpModel files for the whole dataset
                flow_space_recal.HPaggregation(
                    os.path.join(env['BASECALLER_RESULTS'],"recalibration"),
                    env['recalibArgs'])

                hptable = os.path.join(env['BASECALLER_RESULTS'], "recalibration", "hpTable.txt")
                printtime("hptable: %s" % hptable)

                additional_basecallerArgs  = " --calibration-file " + hptable
                additional_basecallerArgs += " --phase-estimation-file " + os.path.join(env['BASECALLER_RESULTS'], "recalibration", "BaseCaller.json")
                additional_basecallerArgs += " --model-file " + os.path.join(env['BASECALLER_RESULTS'], "recalibration", "hpModel.txt")
예제 #3
0
                        os.path.join(env['BASECALLER_RESULTS'],
                                     "recalibration", 'BaseCaller.json'), 'r')
                    chipflow = json.load(c)
                    c.close()
                except:
                    traceback.print_exc()
                    raise

                # Call Calibration module to process training BAM files if we have some
                if len(calibration_input_bams) > 0:
                    calibration_args = env['recalibArgs']
                    if calibration_mode == "blind_recal":
                        calibration_args += " --blind-fit on --load-unmapped on"

                    flow_space_recal.calibrate(env['BASECALLER_RESULTS'],
                                               calibration_input_bams,
                                               calibration_args, chipflow)

                    additional_basecallerArgs  += " --calibration-json " + \
                        os.path.join(env['BASECALLER_RESULTS'], "Calibration.json")

                printtime("Finished Recalibration")
                add_status("Recalibration", 0)
            except:
                traceback.print_exc()
                add_status("Recalibration", 1)
                printtime("ERROR: Recalibration failed")
                sys.exit(1)

        # ---------------------------------------------------------------------------
        # Finished with Calibration workflow - on to base calling
예제 #4
0
                        do_sorting=False,
                        do_mark_duplicates=False,
                        do_indexing=False,
                        output_dir=RECALIBRATION_RESULTS,
                        output_basename=dataset['file_prefix'])

                # Do not call Calibration if we did not generate any aligned input BAMs but gracefully continue
                additional_basecallerArgs += " --phase-estimation-file " + os.path.join(env['BASECALLER_RESULTS'], "recalibration", "BaseCaller.json")
                if env['doBaseRecal'] == "panel_recal":
                    additional_basecallerArgs += " --calibration-panel /opt/ion/config/datasets_calibration.json"
                    
                if len(calibration_input_bams)>0:
                    # Call Calibration module to process aligned training BAM files
                    flow_space_recal.calibrate(
                        env['BASECALLER_RESULTS'],
                        calibration_input_bams,
                        env['recalibArgs'],
                        chipflow)
                
                    additional_basecallerArgs  += " --calibration-json " + os.path.join(env['BASECALLER_RESULTS'],"Calibration.json")
                    
                printtime("Finished Recalibration")
                add_status("Recalibration", 0)
            except:
                traceback.print_exc()
                add_status("Recalibration", 1)
                printtime ("ERROR: Recalibration failed")
                sys.exit(1)

        else:
            printtime("DEBUG: Flow Space Recalibration is disabled")