dimspy.portals package

Submodules

dimspy.portals.hdf5_portal module

The PeakList and PeakMatrix HDF5 portals.

New in version 0.1.

dimspy.portals.hdf5_portal.save_peaklists_as_hdf5(pkls, file_name)

Saves multiple peaklists in HDF5 file.

Parameters:
  • pkls – the target list of peaklist objects
  • file_name – name of the file to export data

To incorporate with different dtypes in the attribute matrix, this portal converts all the arribute values into fix-lenght strings for HDF5 data tables storage. The order of the peaklists will be retained.

dimspy.portals.hdf5_portal.load_peaklists_from_hdf5(file_name)

Loads a list of peaklists from HDF5 file.

Parameters:file_name – name of the file to import data
Return type:list

The values in HDF5 data tables are automatically converted to their original dtypes before loading in the the peaklist.

dimspy.portals.hdf5_portal.save_peak_matrix_as_hdf5(pm, file_name)

Saves a peak matrix in HDF5 file.

Parameters:
  • pm – the target peak matrix object
  • file_name – name of the file to export data

The order of the attributes and flags will be retained.

dimspy.portals.hdf5_portal.load_peak_matrix_from_hdf5(file_name)

Loads a peak matrix from HDF5 file.

Parameters:file_name – name of the file to import data
Return type:PeakMatrix object

dimspy.portals.mzml_portal module

class dimspy.portals.mzml_portal.Mzml(fname='', archive=None)
run()
headers()
peaklist(scan_id, mode_noise='median')
peaklists(scan_ids, mode='median')
headers_scan_ids(n=None)
tics()
extra_info(scan_id)

dimspy.portals.paths module

dimspy.portals.paths.check_paths(tsv, source)

dimspy.portals.thermo_raw_portal module

dimspy.portals.thermo_raw_portal.mz_range_from_header(h)
class dimspy.portals.thermo_raw_portal.ThermoRaw(fname)
headers()
headers_scan_ids()
peaklist(scan_id, mode_noise='noise_packets')
peaklists(scan_ids, mode_noise='noise_packets')
close()

dimspy.portals.txt_portal module

The PeakList and PeakMatrix plain text portals.

New in version 0.1.

dimspy.portals.txt_portal.save_peaklist_as_txt(pkl, file_name, *args, **kwargs)

Saves a peaklist in plain text file.

Parameters:
  • pkl – the target peaklist object
  • file_name – name of the file to export data
  • args – arguments to be passed to PeakList.to_str
  • kwargs – keyword arguments to be passed to PeakList.to_str
dimspy.portals.txt_portal.load_peaklist_from_txt(file_name, ID, delimiter=', ', flag_names='auto', has_flag_col=True)

Loads a peaklist from plain text file.

Parameters:
  • file_name – name of the file to import data
  • ID – ID of the loaded peaklist
  • delimiter – delimiter of the text lines. Default = ‘,’, i.e., CSV format
  • flag_names – names of the flag attributes. Default = ‘auto’, indicating all the attribute names ends with “_flag” will be treated as flag attibute. Provide None to indicate no flag attributes
  • has_flag_col – whether the text file contains the overall “flags” column. If True, it’s values will be discarded. The overall flags of the new peaklist will be calculated automatically. Default = True
Return type:

PeakList object
dimspy.portals.txt_portal.save_peak_matrix_as_txt(pm, file_name, *args, **kwargs)

Saves a peak matrix in plain text file.

Parameters:
  • pm – the target peak matrix object
  • file_name – name of the file to export data
  • args – arguments to be passed to PeakMatrix.to_str
  • kwargs – keyword arguments to be passed to PeakMatrix.to_str
dimspy.portals.txt_portal.load_peak_matrix_from_txt(file_name, delimiter='\t', transposed=False, comprehensive=False)

Loads a peak matrix from plain text file.

Parameters:
  • file_name – name of the file to import data
  • delimiter – delimiter of the text lines. Default = ‘ ‘, i.e., TSV format
  • transposed – whether the attribute matrix has been transposed during the export. Default = False
  • comprehensive – whether the comprehensive information has been included during the export. Default = False
Return type:

PeakMatrix object

Module contents