How to use pyteomics - 10 common examples

def _load_fasta(db, id_regex):
    prot_dict = dict()
    for header, seq in fasta.read(db):
        seq = seq.replace("I", "L").upper()  # convert DB sequence I -> L
        prot_id = header.split()[0]
        if id_regex is not None:
            find_id = re.findall(id_regex, header)
            if len(find_id) > 0:
                prot_id = find_id[0]
        prot_dict[prot_id] = seq

    return prot_dict

"""
	Calculate precursor mass and mz for given peptide and modification list,
	using Pyteomics.

	peptide: stripped peptide sequence
	modifications: MS2PIP-style formatted modifications list (e.g.
	`0|Acetyl|2|Oxidation`)
	mass_shifts: dictionary with `modification_name -> mass_shift` pairs

	Returns: tuple(prec_mass, prec_mz)

	Note: This method does not use the build-in Pyteomics modification handling, as
	that would require a known atomic composition of the modification.
	"""
	charge = int(charge)
	unmodified_mass = mass.fast_mass(peptide)
	mods_massses = sum([mass_shifts[mod] for mod in modifications.split('|')[1::2]])
	prec_mass = unmodified_mass + mods_massses
	prec_mz = (prec_mass + charge * PROTON_MASS) / charge
	return prec_mass, prec_mz

for each in scanFileNumber:
            if each[0] in scanDict.keys():
                scanDict[each[0]].append(int(each[1]))
            else:
                scanDict[each[0]] = [int(each[1])]
        # End of Reading Scans from PSM file
        
        # inputPath = sys.argv[1]
        inputPath = args.msms
        ##outPath = "/".join(sys.argv[3].split("/")[:-1])
        # outPath = sys.argv[3]
        outPath = args.out
        ##outFile = sys.argv[3].split("/")[-1]
        allScanList = []
        # Read all scan numbers using indexedmzML/indexList/index/offset tags
        for k in mzml.read(inputPath).iterfind('indexedmzML/indexList/index/offset'):
            if re.search("scan=(\d+)", k['idRef']):
                a = re.search("scan=(\d+)", k['idRef'])
                allScanList.append(int(a.group(1)))
        allScanList = list(set(allScanList))
        # End of Reading mzML file
        # fraction_name = sys.argv[4]
        fraction_name = args.filestring
        if fraction_name in scanDict.keys():
            scansInList = scanDict[fraction_name]
        else:
            scansInList = []
        scansNotInList = list(set(allScanList) - set(scansInList))
        flag = 0
        if removeORretain == "remove":
            scan2retain = scansNotInList
            scan2retain = list(set(scan2retain))

import numpy as np

from six import string_types as basestring

from .scan import (
    ScanFileMetadataBase, RandomAccessScanSource, ScanDataSource,
    PrecursorInformation, _FakeGroupedScanIteratorImpl,
    ChargeNotProvided)

from .metadata.file_information import (
    FileInformation, MS_MSn_Spectrum)

from ._compression import test_if_file_has_fast_random_access


class _MGFParser(mgf.IndexedMGF):

    def parse_charge(self, charge_text, list_only=False):
        '''Pyteomics _parse_charge is very general-purpose, and
        can't be sped up, so we specialize it here.'''
        try:
            if not list_only:
                return int(charge_text.replace('+', ''))
            return list(map(self.parse_charge, charge_text.split(" ")))
        except Exception:
            if '-' in charge_text:
                return int(charge_text.replace("-", '')) * -1
            raise


class _MGFMetadata(ScanFileMetadataBase):
    """Objects implementing this interface can describe the original source

if word == 'P':
                values['peak_mode'] = 'profile'
            else:
                values['peak_mode'] = 'centroid'
            word = words[i]
            i += 1

        ionization_info = ionization_pat.search(word)
        if ionization_info is not None:
            values['ionization'] = ionization_info.group(0)
            word = words[i]
            i += 1

        cv_info = compensation_voltage_pat.search(word)
        if cv_info is not None:
            values['compensation_voltage'] = unitfloat(cv_info.group(1), None)
            word = words[i]
            i += 1

        return values
    except IndexError:
        return values

def _acquisition_information(self, scan):
        fline = self._filter_string(scan)
        event = self._get_scan_event(scan)
        trailer_extras = self._trailer_values(scan)
        traits = {
            'preset scan configuration': event,
            'filter string': fline,
        }
        cv = fline.get("compensation_voltage")
        if cv is not None:
            traits[FAIMS_compensation_voltage] = cv
        event = ScanEventInformation(
            self._scan_time(scan),
            injection_time=unitfloat(trailer_extras.get(
                'Ion Injection Time (ms)', 0.0), 'millisecond'),
            window_list=[ScanWindow(
                fline.get("scan_window")[0], fline.get("scan_window")[1])],
            traits=traits)
        return ScanAcquisitionInformation("no combination", [event])

combination = "no combination"
        elif "sum of spectra" in scan_list_struct:
            combination = "sum of spectra"
        elif "median of spectra" in scan_list_struct:
            combination = "median of spectra"
        elif "mean of spectra" in scan_list_struct:
            combination = "mean of spectra"
        scan_info['combination'] = combination
        scan_info_scan_list = []
        misplaced_FAIMS_value = scan.get(FAIMS_compensation_voltage.name, None)
        for i, scan_ in enumerate(scan_list_struct.get("scan", [])):
            scan_ = scan_.copy()
            if misplaced_FAIMS_value is not None and i == 0:
                scan[FAIMS_compensation_voltage.name] = misplaced_FAIMS_value
            struct = {}
            struct['start_time'] = scan_.pop('scan start time', unitfloat(0, 'minute'))
            struct['injection_time'] = scan_.pop("ion injection time", unitfloat(0, 'millisecond'))
            windows = []
            for window in scan_.pop("scanWindowList", {}).get("scanWindow", []):
                windows.append(ScanWindow(
                    window['scan window lower limit'],
                    window['scan window upper limit']))
            struct['window_list'] = windows
            scan_.pop("instrumentConfigurationRef", None)
            struct['traits'] = scan_
            scan_info_scan_list.append(ScanEventInformation(**struct))
        scan_info['scan_list'] = scan_info_scan_list
        return ScanAcquisitionInformation(**scan_info)

elif "sum of spectra" in scan_list_struct:
            combination = "sum of spectra"
        elif "median of spectra" in scan_list_struct:
            combination = "median of spectra"
        elif "mean of spectra" in scan_list_struct:
            combination = "mean of spectra"
        scan_info['combination'] = combination
        scan_info_scan_list = []
        misplaced_FAIMS_value = scan.get(FAIMS_compensation_voltage.name, None)
        for i, scan_ in enumerate(scan_list_struct.get("scan", [])):
            scan_ = scan_.copy()
            if misplaced_FAIMS_value is not None and i == 0:
                scan[FAIMS_compensation_voltage.name] = misplaced_FAIMS_value
            struct = {}
            struct['start_time'] = scan_.pop('scan start time', unitfloat(0, 'minute'))
            struct['injection_time'] = scan_.pop("ion injection time", unitfloat(0, 'millisecond'))
            windows = []
            for window in scan_.pop("scanWindowList", {}).get("scanWindow", []):
                windows.append(ScanWindow(
                    window['scan window lower limit'],
                    window['scan window upper limit']))
            struct['window_list'] = windows
            scan_.pop("instrumentConfigurationRef", None)
            struct['traits'] = scan_
            scan_info_scan_list.append(ScanEventInformation(**struct))
        scan_info['scan_list'] = scan_info_scan_list
        return ScanAcquisitionInformation(**scan_info)

def _acquisition_information(self, scan):
        fline = self._filter_string(scan)
        event = self._get_scan_event(scan)
        trailer_extras = self._trailer_values(scan)
        traits = {
            'preset scan configuration': event,
            'filter string': fline,
        }
        cv = fline.get("compensation_voltage")
        if cv is not None:
            traits[FAIMS_compensation_voltage] = cv
        event = ScanEventInformation(
            self._scan_time(scan),
            injection_time=unitfloat(trailer_extras.get('Ion Injection Time (ms)', 0.0), 'millisecond'),
            window_list=[ScanWindow(
                fline.get("scan_window")[0], fline.get("scan_window")[1])], traits=traits)
        return ScanAcquisitionInformation("no combination", [event])

def generate_aa_comp():
    """
    >>> aa_comp = generate_aa_comp()
    >>> aa_comp["M"]
    Composition({'H': 9, 'C': 5, 'S': 1, 'O': 1, 'N': 1})
    >>> aa_comp["Z"]
    Composition({'H': 9, 'C': 5, 'S': 1, 'O': 2, 'N': 1})
    """
    db = pyteomics.mass.Unimod()
    aa_comp = dict(pyteomics.mass.std_aa_comp)
    s = db.by_title("Oxidation")["composition"]
    aa_comp["Z"] = aa_comp["M"] + s
    s = db.by_title("Carbamidomethyl")["composition"]
    aa_comp["C"] = aa_comp["C"] + s
    return aa_comp