How to use ms2pip - 10 common examples

modfile2,
    PTMmap,
    model,
    fragerror,
    tableau,
):
    """
	Function for each worker to process a list of spectra. Each peptide's
	sequence is extracted from the mgf file. Then models are chosen based on
	model. PTMmap, Ntermmap and Ctermmap determine the modifications
	applied to each peptide sequence and the spectrum is predicted. Then either
	the feature vectors are returned, or a DataFrame with the predicted and
	empirical intensities.
	"""

    ms2pip_pyx.ms2pip_init(
        bytearray(afile.encode()),
        bytearray(modfile.encode()),
        bytearray(modfile2.encode()),
    )

    # transform pandas datastructure into dictionary for easy access
    if "ce" in data.columns:
        specdict = (
            data[["spec_id", "peptide", "modifications", "ce"]]
            .set_index("spec_id")
            .to_dict()
        )
        ces = specdict["ce"]
    else:
        specdict = (
            data[["spec_id", "peptide", "modifications"]].set_index("spec_id").to_dict()

def process_peptides(worker_num, data, afile, modfile, modfile2, PTMmap, model):
    """
	Function for each worker to process a list of peptides. The models are
	chosen based on model. PTMmap, Ntermmap and Ctermmap determine the
	modifications applied to each peptide sequence. Returns the predicted
	spectra for all the peptides.
	"""

    ms2pip_pyx.ms2pip_init(
        bytearray(afile.encode()),
        bytearray(modfile.encode()),
        bytearray(modfile2.encode()),
    )

    pcount = 0

    # Prepare output variables
    mz_buf = []
    prediction_buf = []
    peplen_buf = []
    charge_buf = []
    pepid_buf = []

    # transform pandas dataframe into dictionary for easy access
    if "ce" in data.columns:

output_filename="{}".format(params['output_filename']),
                write_mode=write_mode,
            )

        if 'mgf' in params['output_filetype']:
            logging.info("Writing MGF file")
            spectrum_output.write_mgf(
                all_preds,
                peprec=peprec_batch,
                output_filename="{}".format(params['output_filename']),
                write_mode=write_mode
            )

        if 'bibliospec' in params['output_filetype']:
            logging.info("Writing BiblioSpec SSL and MS2 files")
            spectrum_output.write_bibliospec(
                all_preds,
                peprec_batch,
                ms2pip_params,
                output_filename="{}".format(params['output_filename']),
                write_mode=write_mode
            )

        if 'spectronaut' in params['output_filetype']:
            logging.info("Writing Spectronaut CSV file")
            spectrum_output.write_spectronaut(
                all_preds,
                peprec_batch,
                ms2pip_params,
                output_filename="{}".format(params['output_filename']),
                write_mode=write_mode
            )

if not return_results:
            if "mgf" in out_formats:
                print("writing MGF file {}_predictions.mgf...".format(output_filename))
                spectrum_output.write_mgf(
                    all_preds, peprec=data, output_filename=output_filename
                )

            if "msp" in out_formats:
                print("writing MSP file {}_predictions.msp...".format(output_filename))
                spectrum_output.write_msp(
                    all_preds, data, output_filename=output_filename
                )

            if "bibliospec" in out_formats:
                print("writing SSL/MS2 files...")
                spectrum_output.write_bibliospec(
                    all_preds, data, params, output_filename=output_filename
                )

            if "spectronaut" in out_formats:
                print("writing Spectronaut CSV files...")
                spectrum_output.write_spectronaut(
                    all_preds, data, params, output_filename=output_filename
                )

            if "csv" in out_formats:
                print("writing CSV {}_predictions.csv...".format(output_filename))
                all_preds.to_csv(
                    "{}_predictions.csv".format(output_filename), index=False
                )

            sys.stdout.write("done!\n")

]
            ionnumbers.extend([x + 1 for x in range(pl - 1)] * num_ion_types)
            charges.extend([charge_bufs[pi]] * (num_ion_types * (pl - 1)))
            pepids.extend([pepid_bufs[pi]] * (num_ion_types * (pl - 1)))
        all_preds = pd.DataFrame()
        all_preds["spec_id"] = pepids
        all_preds["charge"] = charges
        all_preds["ion"] = ions
        all_preds["ionnumber"] = ionnumbers
        all_preds["mz"] = np.concatenate(mz_bufs, axis=None)
        all_preds["prediction"] = np.concatenate(prediction_bufs, axis=None)

        if not return_results:
            if "mgf" in out_formats:
                print("writing MGF file {}_predictions.mgf...".format(output_filename))
                spectrum_output.write_mgf(
                    all_preds, peprec=data, output_filename=output_filename
                )

            if "msp" in out_formats:
                print("writing MSP file {}_predictions.msp...".format(output_filename))
                spectrum_output.write_msp(
                    all_preds, data, output_filename=output_filename
                )

            if "bibliospec" in out_formats:
                print("writing SSL/MS2 files...")
                spectrum_output.write_bibliospec(
                    all_preds, data, params, output_filename=output_filename
                )

            if "spectronaut" in out_formats:

output_filename="{}_unmodified".format(params['output_filename']),
                write_mode=write_mode,
            )
            """

            logging.info("Writing MSP file")
            spectrum_output.write_msp(
                all_preds,
                peprec_batch,
                output_filename="{}".format(params['output_filename']),
                write_mode=write_mode,
            )

        if 'mgf' in params['output_filetype']:
            logging.info("Writing MGF file")
            spectrum_output.write_mgf(
                all_preds,
                peprec=peprec_batch,
                output_filename="{}".format(params['output_filename']),
                write_mode=write_mode
            )

        if 'bibliospec' in params['output_filetype']:
            logging.info("Writing BiblioSpec SSL and MS2 files")
            spectrum_output.write_bibliospec(
                all_preds,
                peprec_batch,
                ms2pip_params,
                output_filename="{}".format(params['output_filename']),
                write_mode=write_mode
            )

mode=write_mode, append=append, min_itemsize=50
            )

        if 'msp' in params['output_filetype']:
            """
            logging.info("Writing MSP file with unmodified peptides")
            write_msp(
                all_preds,
                peprec_batch[peprec_batch['modifications'] == '-'],
                output_filename="{}_unmodified".format(params['output_filename']),
                write_mode=write_mode,
            )
            """

            logging.info("Writing MSP file")
            spectrum_output.write_msp(
                all_preds,
                peprec_batch,
                output_filename="{}".format(params['output_filename']),
                write_mode=write_mode,
            )

        if 'mgf' in params['output_filetype']:
            logging.info("Writing MGF file")
            spectrum_output.write_mgf(
                all_preds,
                peprec=peprec_batch,
                output_filename="{}".format(params['output_filename']),
                write_mode=write_mode
            )

        if 'bibliospec' in params['output_filetype']:

all_preds["charge"] = charges
        all_preds["ion"] = ions
        all_preds["ionnumber"] = ionnumbers
        all_preds["mz"] = np.concatenate(mz_bufs, axis=None)
        all_preds["prediction"] = np.concatenate(prediction_bufs, axis=None)

        if not return_results:
            if "mgf" in out_formats:
                print("writing MGF file {}_predictions.mgf...".format(output_filename))
                spectrum_output.write_mgf(
                    all_preds, peprec=data, output_filename=output_filename
                )

            if "msp" in out_formats:
                print("writing MSP file {}_predictions.msp...".format(output_filename))
                spectrum_output.write_msp(
                    all_preds, data, output_filename=output_filename
                )

            if "bibliospec" in out_formats:
                print("writing SSL/MS2 files...")
                spectrum_output.write_bibliospec(
                    all_preds, data, params, output_filename=output_filename
                )

            if "spectronaut" in out_formats:
                print("writing Spectronaut CSV files...")
                spectrum_output.write_spectronaut(
                    all_preds, data, params, output_filename=output_filename
                )

            if "csv" in out_formats:

write_mode=write_mode
            )

        if 'bibliospec' in params['output_filetype']:
            logging.info("Writing BiblioSpec SSL and MS2 files")
            spectrum_output.write_bibliospec(
                all_preds,
                peprec_batch,
                ms2pip_params,
                output_filename="{}".format(params['output_filename']),
                write_mode=write_mode
            )

        if 'spectronaut' in params['output_filetype']:
            logging.info("Writing Spectronaut CSV file")
            spectrum_output.write_spectronaut(
                all_preds,
                peprec_batch,
                ms2pip_params,
                output_filename="{}".format(params['output_filename']),
                write_mode=write_mode
            )

        del all_preds
        del peprec_batch

if "msp" in out_formats:
                print("writing MSP file {}_predictions.msp...".format(output_filename))
                spectrum_output.write_msp(
                    all_preds, data, output_filename=output_filename
                )

            if "bibliospec" in out_formats:
                print("writing SSL/MS2 files...")
                spectrum_output.write_bibliospec(
                    all_preds, data, params, output_filename=output_filename
                )

            if "spectronaut" in out_formats:
                print("writing Spectronaut CSV files...")
                spectrum_output.write_spectronaut(
                    all_preds, data, params, output_filename=output_filename
                )

            if "csv" in out_formats:
                print("writing CSV {}_predictions.csv...".format(output_filename))
                all_preds.to_csv(
                    "{}_predictions.csv".format(output_filename), index=False
                )

            sys.stdout.write("done!\n")
        else:
            return all_preds