diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle index d261d2c..40b9ba1 100644 Binary files a/docs/build/doctrees/environment.pickle and b/docs/build/doctrees/environment.pickle differ diff --git a/docs/build/doctrees/pigeon.doctree b/docs/build/doctrees/pigeon.doctree index 855d3b2..a0855cf 100644 Binary files a/docs/build/doctrees/pigeon.doctree and b/docs/build/doctrees/pigeon.doctree differ diff --git a/docs/build/html/_sources/pigeon.rst.txt b/docs/build/html/_sources/pigeon.rst.txt index ea03987..cd6892e 100644 --- a/docs/build/html/_sources/pigeon.rst.txt +++ b/docs/build/html/_sources/pigeon.rst.txt @@ -2,7 +2,7 @@ PIGEON ====== -**PIGEON** (Peptide ID Generation for Exchange Of Nuclei) is a stand-only program that takes in a list of peptide pool csv +**pigeon** is a stand-only program that takes in a list of peptide pool csv and outputs a cleaned csv of pooled data. It also outputs a rangeslist table for merge in FEATHER. CMD Options @@ -11,8 +11,7 @@ CMD Options Type ``pigeon --help`` to see the following options: | ``--t``, ``--table``: Path(s) to input csv. Required -| ``--b``, ``--batch``: -| ``--o``, ``--out``: path to output csv. Default: 'CLEAN.csv' +| ``--o``, ``--out``: path to output csv, if any. | ``--p``, ``--plots``: directory for output plots. Default: './csvplots' | ``--ov``, ``--overlap``: flag specifying how to treat overlapping duplicates. Options: 'keep', 'drop', 'select' (or any other). Default: 'select' | ``--r``, ``--rangeslist``: path to output rangeslist, if any. @@ -25,11 +24,10 @@ Type ``pigeon --help`` to see the following options: Default inputs | ``--t`` (list of peptide pool csvs) -| ``--b`` (table for batched data. Each row contains 'name' string for protein, then all pool csvs corresponding to that pool) Default outputs -| ``--o`` (batched and cleaned peptide pool csv): ``CLEAN.csv`` +| ``--o`` (batched and cleaned peptide pool csv) | ``--r`` (rangeslist table for merge in post-PIGEON) In the plot directory, the following files are generated: @@ -72,4 +70,4 @@ Alternative usage example: .. code-block:: bash - pigeon biotools-cleaner.py --b batch-list.txt --p csvplots --ov select --o select-pooled.csv + pigeon --t pool-1.csv --o select-pooled.csv --r rangeslist.csv diff --git a/docs/build/html/pigeon.html b/docs/build/html/pigeon.html index 10195e3..a8fede7 100644 --- a/docs/build/html/pigeon.html +++ b/docs/build/html/pigeon.html @@ -90,15 +90,14 @@

PIGEON

-

PIGEON (Peptide ID Generation for Exchange Of Nuclei) is a stand-only program that takes in a list of peptide pool csv +

pigeon is a stand-only program that takes in a list of peptide pool csv and outputs a cleaned csv of pooled data. It also outputs a rangeslist table for merge in FEATHER.

CMD Options

Type pigeon --help to see the following options:

--t, --table: Path(s) to input csv. Required
-
--b, --batch:
-
--o, --out: path to output csv. Default: ‘CLEAN.csv’
+
--o, --out: path to output csv, if any.
--p, --plots: directory for output plots. Default: ‘./csvplots’
--ov, --overlap: flag specifying how to treat overlapping duplicates. Options: ‘keep’, ‘drop’, ‘select’ (or any other). Default: ‘select’
--r, --rangeslist: path to output rangeslist, if any.
@@ -111,11 +110,10 @@

CMD Options
--t (list of peptide pool csvs)
-
--b (table for batched data. Each row contains ‘name’ string for protein, then all pool csvs corresponding to that pool)

Default outputs

-
--o (batched and cleaned peptide pool csv): CLEAN.csv
+
--o (batched and cleaned peptide pool csv)
--r (rangeslist table for merge in post-PIGEON)

In the plot directory, the following files are generated:

@@ -155,7 +153,7 @@

Example Usage
pigeon biotools-cleaner.py --b batch-list.txt --p csvplots --ov select --o select-pooled.csv
+
pigeon --t pool-1.csv --o select-pooled.csv --r rangeslist.csv

diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js index 1174b9c..6ea59a2 100644 --- a/docs/build/html/searchindex.js +++ b/docs/build/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["classes", "documentation", "feather", "hdx", "index", "installation", "pigeon", "tutorial", "tutorials/00_ecdhfr_showcase", "tutorials/01_load_data", "tutorials/02_peptide_level_analysis", "tutorials/03_calculate_PFs", "tutorials/04_check_the_fitting", "tutorials/05_plot_the_results"], "filenames": ["classes.rst", "documentation.rst", "feather.rst", "hdx.rst", "index.rst", "installation.rst", "pigeon.rst", "tutorial.rst", "tutorials/00_ecdhfr_showcase.ipynb", "tutorials/01_load_data.ipynb", "tutorials/02_peptide_level_analysis.ipynb", "tutorials/03_calculate_PFs.ipynb", "tutorials/04_check_the_fitting.ipynb", "tutorials/05_plot_the_results.ipynb"], "titles": ["pigeon_feather.data.RangeList", "Documentation", "FEATHER", "HDX/MS", "Welcome to PIGEON-FEATHER\u2019s 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"pigeon_feather.data.SimulatedData.__init__"]], "__init__() (pigeon_feather.data.timepoint method)": [[0, "pigeon_feather.data.Timepoint.__init__"]], "__init__() (pigeon_feather.plot.uptakeplot method)": [[0, "pigeon_feather.plot.UptakePlot.__init__"]], "__init__() (pigeon_feather.plot.uptakeplotscollection method)": [[0, "pigeon_feather.plot.UptakePlotsCollection.__init__"]]}}) \ No newline at end of file diff --git a/docs/source/pigeon.rst b/docs/source/pigeon.rst index ea03987..cd6892e 100644 --- a/docs/source/pigeon.rst +++ b/docs/source/pigeon.rst @@ -2,7 +2,7 @@ PIGEON ====== -**PIGEON** (Peptide ID Generation for Exchange Of Nuclei) is a stand-only program that takes in a list of peptide pool csv +**pigeon** is a stand-only program that takes in a list of peptide pool csv and outputs a cleaned csv of pooled data. It also outputs a rangeslist table for merge in FEATHER. CMD Options @@ -11,8 +11,7 @@ CMD Options Type ``pigeon --help`` to see the following options: | ``--t``, ``--table``: Path(s) to input csv. Required -| ``--b``, ``--batch``: -| ``--o``, ``--out``: path to output csv. Default: 'CLEAN.csv' +| ``--o``, ``--out``: path to output csv, if any. | ``--p``, ``--plots``: directory for output plots. Default: './csvplots' | ``--ov``, ``--overlap``: flag specifying how to treat overlapping duplicates. Options: 'keep', 'drop', 'select' (or any other). Default: 'select' | ``--r``, ``--rangeslist``: path to output rangeslist, if any. @@ -25,11 +24,10 @@ Type ``pigeon --help`` to see the following options: Default inputs | ``--t`` (list of peptide pool csvs) -| ``--b`` (table for batched data. Each row contains 'name' string for protein, then all pool csvs corresponding to that pool) Default outputs -| ``--o`` (batched and cleaned peptide pool csv): ``CLEAN.csv`` +| ``--o`` (batched and cleaned peptide pool csv) | ``--r`` (rangeslist table for merge in post-PIGEON) In the plot directory, the following files are generated: @@ -72,4 +70,4 @@ Alternative usage example: .. code-block:: bash - pigeon biotools-cleaner.py --b batch-list.txt --p csvplots --ov select --o select-pooled.csv + pigeon --t pool-1.csv --o select-pooled.csv --r rangeslist.csv