-
Notifications
You must be signed in to change notification settings - Fork 11
/
searchindex.js
1 lines (1 loc) · 16.6 KB
/
searchindex.js
1
Search.setIndex({ "docnames": ["changelog", "index", "proteobench/modules", "proteobench/proteobench", "proteobench/proteobench.modules", "reference/_autosummary/proteobench.modules", "reference/_autosummary/proteobench.modules.dda_id", "reference/_autosummary/proteobench.modules.dda_id.module_dda_id", "reference/_autosummary/proteobench.modules.dda_quant", "reference/_autosummary/proteobench.modules.dda_quant.datapoint", "reference/_autosummary/proteobench.modules.dda_quant.module", "reference/_autosummary/proteobench.modules.dda_quant.parse", "reference/_autosummary/proteobench.modules.dda_quant.parse_settings", "reference/_autosummary/proteobench.modules.dia_id", "reference/_autosummary/proteobench.modules.dia_quant", "reference/_autosummary/proteobench.modules.dia_quant.module_dia_quant", "reference/_autosummary/proteobench.modules.metaproteomics", "reference/_autosummary/proteobench.modules.metaproteomics.module_metaproteomics", "reference/_autosummary/proteobench.modules.rescoring", "reference/_autosummary/proteobench.modules.rescoring.module_rescoring", "reference/_autosummary/proteobench.modules.template", "reference/_autosummary/proteobench.modules.template.datapoint", "reference/_autosummary/proteobench.modules.template.module", "reference/_autosummary/proteobench.modules.template.parse", "reference/_autosummary/proteobench.modules.template.parse_settings", "reference/_autosummary/proteobench.plot", "reference/_autosummary/webinterface", "reference/_autosummary/webinterface.pages", "reference/_autosummary/webinterface.pages.DDA_ID", "reference/_autosummary/webinterface.pages.DIA_ID", "reference/_autosummary/webinterface.pages.DIA_Quant", "reference/_autosummary/webinterface.pages.Metaproteomics", "reference/_autosummary/webinterface.pages.Rescoring", "reference/_autosummary/webinterface.streamlit_utils", "reference/index", "user_guide/index", "webinterface/modules", "webinterface/webinterface"], "filenames": ["changelog.rst", "index.rst", "proteobench/modules.rst", "proteobench/proteobench.rst", "proteobench/proteobench.modules.rst", "reference/_autosummary/proteobench.modules.rst", "reference/_autosummary/proteobench.modules.dda_id.rst", "reference/_autosummary/proteobench.modules.dda_id.module_dda_id.rst", "reference/_autosummary/proteobench.modules.dda_quant.rst", "reference/_autosummary/proteobench.modules.dda_quant.datapoint.rst", "reference/_autosummary/proteobench.modules.dda_quant.module.rst", "reference/_autosummary/proteobench.modules.dda_quant.parse.rst", "reference/_autosummary/proteobench.modules.dda_quant.parse_settings.rst", "reference/_autosummary/proteobench.modules.dia_id.rst", "reference/_autosummary/proteobench.modules.dia_quant.rst", "reference/_autosummary/proteobench.modules.dia_quant.module_dia_quant.rst", "reference/_autosummary/proteobench.modules.metaproteomics.rst", "reference/_autosummary/proteobench.modules.metaproteomics.module_metaproteomics.rst", "reference/_autosummary/proteobench.modules.rescoring.rst", "reference/_autosummary/proteobench.modules.rescoring.module_rescoring.rst", "reference/_autosummary/proteobench.modules.template.rst", "reference/_autosummary/proteobench.modules.template.datapoint.rst", "reference/_autosummary/proteobench.modules.template.module.rst", "reference/_autosummary/proteobench.modules.template.parse.rst", "reference/_autosummary/proteobench.modules.template.parse_settings.rst", "reference/_autosummary/proteobench.plot.rst", "reference/_autosummary/webinterface.rst", "reference/_autosummary/webinterface.pages.rst", "reference/_autosummary/webinterface.pages.DDA_ID.rst", "reference/_autosummary/webinterface.pages.DIA_ID.rst", "reference/_autosummary/webinterface.pages.DIA_Quant.rst", "reference/_autosummary/webinterface.pages.Metaproteomics.rst", "reference/_autosummary/webinterface.pages.Rescoring.rst", "reference/_autosummary/webinterface.streamlit_utils.rst", "reference/index.rst", "user_guide/index.rst", "webinterface/modules.rst", "webinterface/webinterface.rst"], "titles": ["Change log", "Welcome to ProteoBench\u2019s documentation!", "proteobench", "proteobench package", "proteobench.modules package", "proteobench.modules", "proteobench.modules.dda_id", "proteobench.modules.dda_id.module_dda_id", "proteobench.modules.dda_quant", "proteobench.modules.dda_quant.datapoint", "proteobench.modules.dda_quant.module", "proteobench.modules.dda_quant.parse", "proteobench.modules.dda_quant.parse_settings", "proteobench.modules.dia_id", "proteobench.modules.dia_quant", "proteobench.modules.dia_quant.module_dia_quant", "proteobench.modules.metaproteomics", "proteobench.modules.metaproteomics.module_metaproteomics", "proteobench.modules.rescoring", "proteobench.modules.rescoring.module_rescoring", "proteobench.modules.template", "proteobench.modules.template.datapoint", "proteobench.modules.template.module", "proteobench.modules.template.parse", "proteobench.modules.template.parse_settings", "proteobench.plot", "webinterface", "webinterface.pages", "webinterface.pages.DDA_ID", "webinterface.pages.DIA_ID", "webinterface.pages.DIA_Quant", "webinterface.pages.Metaproteomics", "webinterface.pages.Rescoring", "webinterface.streamlit_utils", "Reference", "User guide", "webinterface", "webinterface package"], "terms": { "todo": 0, "index": [1, 34], "modul": [1, 2, 26, 27, 34, 37], "search": [1, 4, 34], "page": [1, 34], "packag": [2, 35, 36], "subpackag": 2, "io": [], "content": [2, 37], "plot": [4, 35], "dda_id": 4, "submodul": [4, 36], "module_dda_id": 4, "dda_quant": 4, "datapoint": [4, 35], "pars": [4, 35], "parse_set": 4, "dia_id": 4, "dia_quant": 4, "module_dia_qu": 4, "metaproteom": 4, "module_metaproteom": 4, "rescor": 4, "module_rescor": 4, "templat": [4, 35], "moduleinterfac": [3, 4, 35], "add_current_data_point": [3, 4], "benchmark": [3, 4, 35], "generate_datapoint": [3, 4], "generate_intermedi": [3, 4], "load_input_fil": [3, 4], "parseinputsinterfac": [3, 4, 35], "convert_to_standard_format": [3, 4], "is_impl": 4, "mbr": 4, "calculate_missing_quan_prec": 4, "calculate_plot_data": 4, "dump_json_object": 4, "enzyme_nam": 4, "fdr_peptid": 4, "fdr_protein": 4, "fdr_psm": 4, "fragment_tol_unit": 4, "fragment_tol": 4, "generate_id": 4, "id": 4, "is_temporari": 4, "max_pep_length": 4, "min_pep_length": 4, "missed_cleavag": 4, "nr_prec": 4, "precursor_tol": 4, "precursor_tol_unit": 4, "search_engin": 4, "software_vers": 4, "weighted_sum": 4, "strip_sequence_wombat": 4, "parseinput": [4, 35], "parseset": 4, "calculate_benchmarking_metric_1": 4, "calculate_benchmarking_metric_2": 4, "class": [4, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 33, 35], "base": 4, "abc": 4, "abstract": 4, "method": 4, "us": [4, 35], "add": [4, 35], "current": 4, "data": [4, 35], "point": [4, 35], "collect": [4, 35], "run": [4, 35], "comput": 4, "provid": [4, 35], "intermedi": [4, 35], "structur": 4, "calcul": [4, 35], "valu": 4, "from": [4, 35], "upload": [4, 35], "file": [4, 35], "load": 4, "datafram": [4, 35], "depend": 4, "its": [4, 35], "format": [4, 12, 24, 35], "convert": 4, "engin": 4, "output": [4, 35], "gener": [4, 35], "support": 4, "main": [7, 15, 17, 19, 35], "interfac": [7, 15, 17, 19, 35], "bool": [], "return": [], "whether": [], "i": 35, "fulli": [], "implement": 35, "str": [], "none": [], "int": [], "0": [], "fals": [], "da": [], "true": [], "object": 35, "store": [], "df": [], "nr_missing_0": [], "file_nam": [], "librari": [], "within": [], "all_datapoint": [], "current_datapoint": [], "all": [12, 24, 35], "them": [], "empti": [], "Not": [], "clear": [], "why": [], "transpos": [], "here": 35, "input_fil": [], "input_format": [], "user_input": [], "dict": [], "workflow": [], "result": [], "metadata": 35, "filtered_df": [], "replicate_to_raw": [], "take": [], "get": [], "quantif": [], "tupl": [], "measur": [], "reliabl": [], "input_csv": [], "csv": [], "seq": [], "remov": [], "part": [], "peptid": 35, "sequenc": [], "contain": 35, "modif": [], "panda": [], "core": [], "frame": [], "list": [], "avail": [12, 24], "paramet": 35, "given": 35, "databas": [], "experiment": [], "analysi": [], "set": 35, "A": 35, "uniqu": [], "identifi": [], "type": 35, "boolean": [], "flag": [], "indic": [], "temporari": [], "The": 35, "name": [], "experi": [], "version": [], "number": [], "softwar": [], "discoveri": [], "rate": [], "spectrum": [], "match": [], "level": [], "protein": [], "between": [], "wa": [], "enabl": [], "precursor": [], "mass": [], "toler": [], "unit": [], "specifi": [], "either": [], "ppm": [], "fragment": [], "enzym": [], "digest": [], "allow": 35, "miss": [], "cleavag": [], "dure": [], "minimum": [], "length": [], "identif": [], "maximum": [], "weight": [], "sum": [], "score": [], "infer": [], "intermediate_data": [], "first": [], "metric": 35, "dictionari": [], "metric_1": [], "float": [], "second": [], "metric_2": [], "dump": [], "json": 35, "write": [], "represent": [], "append": [], "end": [], "alreadi": [], "exist": [], "attribut": [], "string": [], "compos": [], "timestamp": [], "separ": 35, "underscor": [], "print": [], "stdout": [], "input": [24, 35], "function": [7, 15, 17, 19, 33, 35], "streamlit": [33, 35], "util": 33, "welcom": 35, "proteobench": 35, "can": 35, "python": 35, "usual": 35, "pip": 35, "command": 35, "without": 35, "clone": 35, "repositori": 35, "setup": 35, "script": 35, "git": 35, "http": 35, "github": 35, "com": 35, "cd": 35, "py": 35, "start": 35, "gui": 35, "your": 35, "termin": 35, "follow": 35, "home": 35, "altern": 35, "you": 35, "jupyt": 35, "notebook": 35, "test_workflow": 35, "ipynb": 35, "more": 35, "control": 35, "over": 35, "pleas": 35, "we": 35, "hopefulli": 35, "comprehens": 35, "document": 35, "how": 35, "up": 35, "suggest": 35, "understand": 35, "term": 35, "thei": 35, "ar": 35, "crucial": 35, "compon": 35, "_module_": 35, "code": 35, "definit": 35, "creat": 35, "compar": 35, "_datapoint_": 35, "need": 35, "should": 35, "also": 35, "repres": 35, "_intermediate_": 35, "It": 35, "transform": 35, "annot": 35, "locat": 35, "directori": 35, "differ": 35, "step": 35, "modular": 35, "portabl": 35, "each": 35, "1": 35, "read": 35, "process": 35, "well": 35, "our": 35, "_datapoints_": 35, "2": 35, "standard": 35, "respect": 35, "e": 35, "g": 35, "maxquant": 35, "3": 35, "properti": 35, "acquisit": 35, "fdr": 35, "plotdatapoint": 35, "visual": 35, "5": 35, "defin": 35, "toml": 35, "like": 35, "io_parse_set": 35, "parse_settings_format1": 35, "thi": 35, "meant": 35, "help": 35, "exhaust": 35, "cover": 35, "most": 35, "import": 35, "copi": 35, "folder": 35, "same": 35, "call": 35, "__init__": 35, "just": 35, "my_modul": 35, "my_module_test": 35, "test": 35, "my_module_doc": 35, "my_module_config": 35, "recommend": 35, "keep": 35, "For": 35, "specif": 35, "layout": 35, "streamlit_util": [], "streamlitlogg": [], "hide_streamlit_menu": [], "save_datafram": [], "placehold": [], "logger_nam": [], "accumul": [], "persist": [], "pickup": [], "logger": [], "front": [], "save": [], "cach": [] }, "objects": { "": [[3, 0, 0, "-", "proteobench"], [37, 0, 0, "-", "webinterface"]], "proteobench.modules": [[6, 0, 0, "-", "dda_id"], [13, 0, 0, "-", "dia_id"], [14, 0, 0, "-", "dia_quant"], [16, 0, 0, "-", "metaproteomics"], [18, 0, 0, "-", "rescoring"]], "proteobench.modules.dda_id": [[7, 0, 0, "-", "module_dda_id"]], "proteobench.modules.dia_quant": [[15, 0, 0, "-", "module_dia_quant"]], "proteobench.modules.metaproteomics": [[17, 0, 0, "-", "module_metaproteomics"]], "proteobench.modules.rescoring": [[19, 0, 0, "-", "module_rescoring"]], "proteobench": [[25, 0, 0, "-", "plot"]], "webinterface": [[27, 0, 0, "-", "pages"]], "webinterface.pages": [[28, 0, 0, "-", "DDA_ID"], [29, 0, 0, "-", "DIA_ID"], [30, 0, 0, "-", "DIA_Quant"], [31, 0, 0, "-", "Metaproteomics"], [32, 0, 0, "-", "Rescoring"]] }, "objtypes": { "0": "py:module" }, "objnames": { "0": ["py", "module", "Python module"] }, "titleterms": { "chang": 0, "log": 0, "welcom": 1, "proteobench": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25], "": 1, "document": 1, "indic": 1, "tabl": 1, "packag": [3, 4, 37], "subpackag": [3, 4], "modul": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35], "content": [3, 4], "io": [], "dda_id": [6, 7, 28], "submodul": 37, "module_dda_id": 7, "dda_quant": [8, 9, 10, 11, 12], "datapoint": [9, 21], "pars": [11, 23], "parse_set": [12, 24], "plot": 25, "dia_id": [13, 29], "dia_quant": [14, 15, 30], "module_dia_qu": 15, "metaproteom": [16, 17, 31], "module_metaproteom": 17, "rescor": [18, 19, 32], "module_rescor": 19, "templat": [20, 21, 22, 23, 24], "webinterfac": [26, 27, 28, 29, 30, 31, 32, 33, 36, 37], "page": [27, 28, 29, 30, 31, 32], "streamlit_util": 33, "refer": 34, "user": 35, "guid": 35, "instal": 35, "local": 35, "usag": 35, "develop": 35, "ad": 35, "new": 35, "name": 35, "convent": 35, "programmat": 35, "structur": 35, "checklist": 35, "modifi": 35, "an": 35, "exist": 35, "home": [] }, "envversion": { "sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx": 57 }, "alltitles": { "Change log": [[0, "change-log"]], "Welcome to ProteoBench\u2019s documentation!": [[1, "welcome-to-proteobench-s-documentation"]], "Indices and tables": [[1, "indices-and-tables"]], "proteobench": [[2, "proteobench"]], "Subpackages": [[4, "subpackages"], [3, "subpackages"]], "Module contents": [[4, "module-proteobench.modules"], [3, "module-proteobench"]], "proteobench.modules package": [[4, "proteobench-modules-package"]], "proteobench.modules": [[5, "module-proteobench.modules"]], "proteobench.modules.dda_id": [[6, "module-proteobench.modules.dda_id"]], "proteobench.modules.dda_id.module_dda_id": [[7, "module-proteobench.modules.dda_id.module_dda_id"]], "proteobench.modules.dda_quant": [[8, "module-proteobench.modules.dda_quant"]], "proteobench.modules.dda_quant.datapoint": [[9, "module-proteobench.modules.dda_quant.datapoint"]], "proteobench.modules.dda_quant.module": [[10, "module-proteobench.modules.dda_quant.module"]], "proteobench.modules.dda_quant.parse": [[11, "module-proteobench.modules.dda_quant.parse"]], "proteobench.modules.dda_quant.parse_settings": [[12, "module-proteobench.modules.dda_quant.parse_settings"]], "proteobench.modules.dia_id": [[13, "module-proteobench.modules.dia_id"]], "proteobench.modules.dia_quant": [[14, "module-proteobench.modules.dia_quant"]], "proteobench.modules.dia_quant.module_dia_quant": [[15, "module-proteobench.modules.dia_quant.module_dia_quant"]], "proteobench.modules.metaproteomics": [[16, "module-proteobench.modules.metaproteomics"]], "proteobench.modules.metaproteomics.module_metaproteomics": [[17, "module-proteobench.modules.metaproteomics.module_metaproteomics"]], "proteobench.modules.rescoring": [[18, "module-proteobench.modules.rescoring"]], "proteobench.modules.rescoring.module_rescoring": [[19, "module-proteobench.modules.rescoring.module_rescoring"]], "proteobench.modules.template": [[20, "module-proteobench.modules.template"]], "proteobench.modules.template.datapoint": [[21, "module-proteobench.modules.template.datapoint"]], "proteobench.modules.template.module": [[22, "module-proteobench.modules.template.module"]], "proteobench.modules.template.parse": [[23, "module-proteobench.modules.template.parse"]], "proteobench.modules.template.parse_settings": [[24, "module-proteobench.modules.template.parse_settings"]], "proteobench.plot": [[25, "module-proteobench.plot"]], "webinterface": [[26, "module-webinterface"], [36, "webinterface"]], "webinterface.pages": [[27, "module-webinterface.pages"]], "webinterface.pages.DDA_ID": [[28, "module-webinterface.pages.DDA_ID"]], "webinterface.pages.DIA_ID": [[29, "module-webinterface.pages.DIA_ID"]], "webinterface.pages.DIA_Quant": [[30, "module-webinterface.pages.DIA_Quant"]], "webinterface.pages.Metaproteomics": [[31, "module-webinterface.pages.Metaproteomics"]], "webinterface.pages.Rescoring": [[32, "module-webinterface.pages.Rescoring"]], "webinterface.streamlit_utils": [[33, "module-webinterface.streamlit_utils"]], "Reference": [[34, "reference"]], "Submodules": [[37, "submodules"]], "webinterface package": [[37, "webinterface-package"]], "User guide": [[35, "user-guide"]], "Installation": [[35, "installation"]], "Local usage": [[35, "local-usage"]], "Development": [[35, "development"]], "Adding a new modules": [[35, "adding-a-new-modules"]], "Naming convention": [[35, "naming-convention"]], "Programmatic structure": [[35, "programmatic-structure"]], "Checklist": [[35, "checklist"]], "Modifying an existing module": [[35, "modifying-an-existing-module"]], "proteobench package": [[3, "proteobench-package"]] }, "indexentries": { "module": [[3, "module-proteobench"]], "proteobench": [[3, "module-proteobench"]] } })