Index

A

aggregate() (in module pyXLMS.transform_aggregate) AMINO_ACIDS (in module pyXLMS.constants)

AMINO_ACIDS_1TO3 (in module pyXLMS.constants) AMINO_ACIDS_3TO1 (in module pyXLMS.constants) assert_data_type_same() (in module pyXLMS.transform_util)

C

check_indexing() (in module pyXLMS.data) check_input() (in module pyXLMS.data) check_input_multi() (in module pyXLMS.data) create_crosslink() (in module pyXLMS.data) create_crosslink_from_csm() (in module pyXLMS.data)

create_crosslink_min() (in module pyXLMS.data) create_csm() (in module pyXLMS.data) create_csm_min() (in module pyXLMS.data) create_parser_result() (in module pyXLMS.data) CROSSLINKERS (in module pyXLMS.constants)

D

detect_scout_filetype() (in module pyXLMS.parser_xldbse_scout)

detect_xi_filetype() (in module pyXLMS.parser_xldbse_xi)

F

fasta_title_to_accession() (in module pyXLMS.transform_reannotate_positions) filter_crosslink_type() (in module pyXLMS.transform_filter)

filter_proteins() (in module pyXLMS.transform_filter) filter_target_decoy() (in module pyXLMS.transform_filter) format_sequence() (in module pyXLMS.parser_util)

G

get_available_keys() (in module pyXLMS.transform_util)

get_bool_from_value() (in module pyXLMS.parser_util) get_msannika_crosslink_sequence() (in module pyXLMS.exporter_to_msannika)

M

MODIFICATIONS (in module pyXLMS.constants) modifications_to_str() (in module pyXLMS.transform_util) module pyXLMS pyXLMS.constants pyXLMS.data pyXLMS.exporter pyXLMS.exporter_to_impxfdr pyXLMS.exporter_to_msannika pyXLMS.exporter_to_pyxlinkviewer pyXLMS.exporter_to_xifdr pyXLMS.exporter_to_xinet pyXLMS.exporter_to_xiview pyXLMS.exporter_to_xlinkdb pyXLMS.exporter_to_xlmstools pyXLMS.exporter_to_xmas pyXLMS.exporter_util pyXLMS.parser pyXLMS.parser_util pyXLMS.parser_xldbse_custom pyXLMS.parser_xldbse_maxquant pyXLMS.parser_xldbse_msannika pyXLMS.parser_xldbse_mzid pyXLMS.parser_xldbse_plink pyXLMS.parser_xldbse_scout pyXLMS.parser_xldbse_xi pyXLMS.parser_xldbse_xlinkx pyXLMS.pipelines pyXLMS.transform pyXLMS.transform_aggregate pyXLMS.transform_filter pyXLMS.transform_reannotate_positions pyXLMS.transform_summary pyXLMS.transform_targets_only pyXLMS.transform_to_dataframe pyXLMS.transform_to_proforma pyXLMS.transform_util pyXLMS.transform_validate

P

parse_modifications_from_maxquant_sequence() (in module pyXLMS.parser_xldbse_maxquant) parse_modifications_from_scout_sequence() (in module pyXLMS.parser_xldbse_scout) parse_modifications_from_xi_sequence() (in module pyXLMS.parser_xldbse_xi) parse_peptide() (in module pyXLMS.parser_xldbse_xi) parse_scan_nr_from_mzid() (in module pyXLMS.parser_xldbse_mzid) parse_scan_nr_from_plink() (in module pyXLMS.parser_xldbse_plink) parse_spectrum_file_from_plink() (in module pyXLMS.parser_xldbse_plink) pipeline() (in module pyXLMS.pipelines) pyXLMS module pyXLMS.constants module pyXLMS.data module pyXLMS.exporter module pyXLMS.exporter_to_impxfdr module pyXLMS.exporter_to_msannika module pyXLMS.exporter_to_pyxlinkviewer module pyXLMS.exporter_to_xifdr module pyXLMS.exporter_to_xinet module pyXLMS.exporter_to_xiview module pyXLMS.exporter_to_xlinkdb module pyXLMS.exporter_to_xlmstools module pyXLMS.exporter_to_xmas module pyXLMS.exporter_util module pyXLMS.parser module pyXLMS.parser_util module

pyXLMS.parser_xldbse_custom module pyXLMS.parser_xldbse_maxquant module pyXLMS.parser_xldbse_msannika module pyXLMS.parser_xldbse_mzid module pyXLMS.parser_xldbse_plink module pyXLMS.parser_xldbse_scout module pyXLMS.parser_xldbse_xi module pyXLMS.parser_xldbse_xlinkx module pyXLMS.pipelines module pyXLMS.transform module pyXLMS.transform_aggregate module pyXLMS.transform_filter module pyXLMS.transform_reannotate_positions module pyXLMS.transform_summary module pyXLMS.transform_targets_only module pyXLMS.transform_to_dataframe module pyXLMS.transform_to_proforma module pyXLMS.transform_util module pyXLMS.transform_validate module pyxlms_modification_str_parser() (in module pyXLMS.parser_xldbse_custom)

R

read() (in module pyXLMS.parser) read_custom() (in module pyXLMS.parser_xldbse_custom) read_maxlynx() (in module pyXLMS.parser_xldbse_maxquant) read_maxquant() (in module pyXLMS.parser_xldbse_maxquant) read_msannika() (in module pyXLMS.parser_xldbse_msannika)

read_mzid() (in module pyXLMS.parser_xldbse_mzid) read_plink() (in module pyXLMS.parser_xldbse_plink) read_scout() (in module pyXLMS.parser_xldbse_scout) read_xi() (in module pyXLMS.parser_xldbse_xi) read_xlinkx() (in module pyXLMS.parser_xldbse_xlinkx) reannotate_positions() (in module pyXLMS.transform_reannotate_positions)

S

SCOUT_MODIFICATION_MAPPING (in module pyXLMS.constants)

summary() (in module pyXLMS.transform_summary)

T

targets_only() (in module pyXLMS.transform_targets_only) to_dataframe() (in module pyXLMS.transform_to_dataframe) to_impxfdr() (in module pyXLMS.exporter_to_impxfdr) to_msannika() (in module pyXLMS.exporter_to_msannika) to_proforma() (in module pyXLMS.transform_to_proforma) to_pyxlinkviewer() (in module pyXLMS.exporter_to_pyxlinkviewer)

to_xifdr() (in module pyXLMS.exporter_to_xifdr) to_xinet() (in module pyXLMS.exporter_to_xinet) to_xiview() (in module pyXLMS.exporter_to_xiview) to_xlinkdb() (in module pyXLMS.exporter_to_xlinkdb) to_xlmstools() (in module pyXLMS.exporter_to_xlmstools) to_xmas() (in module pyXLMS.exporter_to_xmas)

U

unique() (in module pyXLMS.transform_aggregate)

V

validate() (in module pyXLMS.transform_validate)

X

XI_MODIFICATION_MAPPING (in module pyXLMS.constants)