Merge pull request bigbio#17 from bigbio/dev

Dev

docs/ae.rst

@@ -74,4 +74,4 @@ We suggest including the following properties in the header:
    (e.g. ``tissue``)
 
 Please check also the differential expression example for more
-information `DE <DE.rst>`__
+information :doc:`de`

docs/conf.py

@@ -17,12 +17,12 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'quantms'
+project = 'quantms.io'
 copyright = '2022, daichengxin, jpfeuffer, timosachenberg, ypriverol'
 author = 'daichengxin, jpfeuffer, timosachenberg, ypriverol'
 
 # The full version, including alpha/beta/rc tags
-release = '1.1.0'
+release = '1.0'
 
 
 # -- General configuration ---------------------------------------------------
@@ -31,6 +31,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    'sphinx.ext.autosectionlabel',
 ]
 
 # Add any paths that contain templates here, relative to this directory.

docs/de.rst

@@ -89,4 +89,4 @@ We suggest including the following properties in the header:
    (e.g. ``adj.pvalue < 0.05``)
 
 A complete example of a quantms output file can be seen
-`here <../include/PXD004683-quantms.csv>`__.
+`here <https://github.com/bigbio/quantms.io/blob/dev/docs/include/PXD004683-quantms.csv>`__.

docs/feature.rst

@@ -24,14 +24,14 @@ Format
 
 Peptide properties and columns:
 
--  ``sequence``: The peptide’s sequence corresponding to the feature, this peptide sequence do not includes posttraslational modifications -> ``string``
+-  ``sequence``: The peptide’s sequence corresponding to the feature, this peptide sequence do not includes post-translational modifications -> ``string``
 -  ``unique``: Indicates whether the peptide sequence is unique for this protein in respect to the searched database -> ``boolean (0/1)``
 -  ``modifications``: A list of modifications for a give peptide ``[modification1, modification2, ...]``. A modification should be
-   recorded as string like `modification definition <README.rst#modifications>`__-> ``list[string]``
+   recorded as string like :ref:`modifications` -> ``list[string]``
 -  ``charge``: The charge assigned by the search engine/software -> ``integer``
 -  ``calc_mass_to_charge``: The PSM’s calculated (theoretical) mass to charge (m/z) -> ``double``
 -  ``exp_mass_to_charge``: The PSM’s experimental mass to charge (m/z) -> ``double``
--  ``peptidoform``: Peptidoform of the PSM. See more `documentation here <Introduction.rst#peptidoform>`__. -> ``string``
+-  ``peptidoform``: Peptidoform of the PSM. See more :ref:`peptidoform` -> ``string``
 -  ``posterior_error_probability``: Posterior Error Probability score from quantms -> ``double``
 -  ``global_qvalue``: Global q-value for the feature for the peptide identification in the experiment -> ``double``
 -  ``is_decoy``: Indicates whether the peptide sequence (coming from the PSM) is decoy -> ``boolean (0/1)``

docs/introduction.rst

@@ -1,14 +1,14 @@
 Introduction to quantms.io
 ======================================
 
-The ``.qms`` folder will contain multiple metadata files that will be
+The ``.qms`` folder will contain multiple files that will be
 used to describe the project, the samples, the data acquisition and the
-data processing. Each of these files will be described in the following
+data processing, in addition to the data files. Each of these files will be described in the following
 sections:
 
 -  :doc:`metadata`: A json file for metadata about the
    analyzed project
--  :doc:`ae` or :doc:`ae`: A csv file based on the MSstats (TODO link) format for either absolute expression or
+-  :doc:`ae` or :doc:`de`: A csv file based on the `MSstats <https://github.com/Vitek-Lab/MSstats>`_ format for either absolute expression or
    differential expression.
 
 Some general rules for all the files:
@@ -77,4 +77,4 @@ This concept is used in the following outputs:
 
 -  :doc:`psm`
 -  :doc:`feature`
--  :doc:`peptide`
+-  :doc:`peptide`

python/quantmsio/quantms_io/commands/absolute_expression_command.py

@@ -1,7 +1,16 @@
 from quantms_io.core.ae import AbsoluteExpressionHander
 import click
+CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
+
+
+@click.group(context_settings=CONTEXT_SETTINGS)
+def cli():
+    """
+    This is the main tool that gives access to all commands.
+    """
+
 @click.command(
-    "convert-ibaq-absolute",
+    "convert_ibaq_absolute",
     short_help="Convert a ibaq_absolute file into a quantms.io file " "format",
 )
 @click.option(
@@ -10,46 +19,54 @@
     required=True,
 )
 @click.option(
-    "--output_folder", help="Folder to generate the df expression file.", required=True
+    "--sdrf_file",
+    help="the sdrf_file path",
+    required=True,
 )
-@click.option("--output_prefix_file", help="Prefix of the df expression file", required=False)
 @click.option(
-    "--generate_project",
-    help="Generate project.json for pride project, Otherwise, False",
+    "--project_file",
+    help="quantms.io project file",
     required=False,
-    is_flag=True,
 )
+@click.option(
+    "--output_folder", help="Folder to generate the df expression file.", required=True
+)
+@click.option("--output_prefix_file", help="Prefix of the df expression file", required=False)
 @click.option(
     "--delete_existing", help="Delete existing files in the output folder", is_flag=True
 )
-@click.option("--project_file", help="quantms.io project file", required=False)
-def convert_ibaq_absolute(
+@click.pass_context
+def convert_ibaq_absolute(ctx,
     ibaq_file:str,
+    sdrf_file:str,
+    project_file: str,
     output_folder: str,
     output_prefix_file: str,
-    generate_project: bool = True,
     delete_existing: bool = True,
-    project_file:str = None,
     ):
     """
     Convert a IBAQ absolute file into a quantms.io file format. The file definition is available in the docs
     https://github.com/bigbio/quantms.io/blob/main/docs/AE.md.
     :param ibaq_file: IBAQ file
+    :param sdrf_file: sdrf file
     :param project_file: quantms.io project file
     :param output_folder: Folder to generate the df expression file.
     :param output_prefix_file: Prefix of the df expression file
-    :param generate_project: "Generate project.json for pride project, Otherwise, False"
     :param delete_existing: Delete existing files in the output folder
     :return: none
     """
-    de_handler = AbsoluteExpressionHander()
-    if generate_project:
-        de_handler.load_project_file(project_file)
-    de_handler.load_ibaq_file(ibaq_file)
-    de_handler.convert_ibaq_to_quantms(
+    ae_handler = AbsoluteExpressionHander()
+    if project_file:
+        ae_handler.load_project_file(project_file)
+    ae_handler.load_ibaq_file(ibaq_file)
+    ae_handler.load_sdrf_file(sdrf_file)
+    ae_handler.convert_ibaq_to_quantms(
         output_folder=output_folder,
-        output_prefix_file_prefix=output_prefix_file,
+        output_file_prefix=output_prefix_file,
         delete_existing=delete_existing,
     )
-    if generate_project:
-        de_handler.update_project_file(project_file)
+
+cli.add_command(convert_ibaq_absolute)
+
+if __name__ == '__main__':
+    cli()

python/quantmsio/quantms_io/commands/attach_file_command.py

@@ -0,0 +1,37 @@
+from quantms_io.core.tools import register_file_to_json
+import click
+CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
+
+
+@click.group(context_settings=CONTEXT_SETTINGS)
+def cli():
+    """
+    This is the main tool that gives access to all commands.
+    """
+
+
+@click.command("attach_file_to_json", short_help="Register the file to project.json.",)
+@click.option("--project_file", help="the project.json file", required=True)
+@click.option("--attach_file", help="The path of the file that will be registered", required=True)
+@click.option("--category", type=click.Choice(['feature_file', 'psm_file', 'differential_file',
+                                              'absolute_file'], case_sensitive=False),
+              help="The type of file that will be registered.", required=True)
+@click.option("--replace_existing", help="Whether to delete old files", is_flag=True)
+@click.pass_context
+def attach_file_to_json(ctx, project_file, attach_file, category, replace_existing):
+    """
+    Register the file with project.json
+    :param project_file: the project.json file path
+    :param attach_file: The path of the file that will be registered
+    :param category: The type of file that will be registered
+    :param replace_existing Whether to delete old files
+    :return: none
+    """
+    register_file_to_json(project_file, attach_file,
+                          category, replace_existing)
+
+
+cli.add_command(attach_file_to_json)
+
+if __name__ == '__main__':
+    cli()

python/quantmsio/quantms_io/commands/differential_expression_command.py

@@ -1,19 +1,30 @@
 import click
 
 from quantms_io.core.de import DifferentialExpressionHandler
+CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
 
 
+@click.group(context_settings=CONTEXT_SETTINGS)
+def cli():
+    """
+    This is the main tool that gives access to all commands.
+    """
+
 @click.command(
-    "convert-msstats-differential",
+    "convert_msstats_differential",
     short_help="Convert a MSstats differential file into a quantms.io file " "format",
 )
 @click.option("--msstats_file", help="MSstats differential file", required=True)
-@click.option("--project_file", help="quantms.io project file", required=False)
 @click.option(
     "--sdrf_file",
     help="the SDRF file needed to extract some of the metadata",
     required=True,
 )
+@click.option(
+    "--project_file",
+    help="quantms.io project file",
+    required=False,
+)
 @click.option(
     "--fdr_threshold",
     help="FDR threshold to use to filter the results",
@@ -24,44 +35,38 @@
     "--output_folder", help="Folder to generate the df expression file.", required=True
 )
 @click.option("--output_prefix_file", help="Prefix of the df expression file", required=False)
-@click.option(
-    "--generate_project",
-    help="Generate project.json for pride project, Otherwise, False",
-    required=False,
-    is_flag=True,
-)
 @click.option(
     "--delete_existing", help="Delete existing files in the output folder", is_flag=True
 )
+@click.pass_context
 def convert_msstats_differential(
+    ctx,
     msstats_file: str,
     sdrf_file: str,
+    project_file:str,
     fdr_threshold: float,
     output_folder: str,
     output_prefix_file: str,
-    generate_project: bool= True,
     delete_existing: bool=True,
-    project_file: str = None,
 ):
     """
     Convert a MSstats differential file into a quantms.io file format. The file definition is available in the docs
     https://github.com/bigbio/quantms.io/blob/main/docs/DE.md.
     :param msstats_file: MSstats differential file
-    :param project_file: quantms.io project file
     :param sdrf_file: the SDRF file needed to extract some of the metadata
+    :param project_file: quantms.io project file
     :param output_folder: Folder to generate the df expression file.
     :param output_prefix_file: Prefix of the df expression file
     :param delete_existing: Delete existing files in the output folder
     :param fdr_threshold: FDR threshold to use to filter the results
-    :param generate_project: "Generate project.json for pride project, Otherwise, False"
     :return: none
     """
 
-    if msstats_file is None or project_file is None or output_folder is None:
+    if msstats_file is None or sdrf_file is None or output_folder is None:
         raise click.UsageError("Please provide all the required parameters")
 
     de_handler = DifferentialExpressionHandler()
-    if generate_project:
+    if project_file:
         de_handler.load_project_file(project_file)
     de_handler.load_msstats_file(msstats_file)
     de_handler.load_sdrf_file(sdrf_file)
@@ -71,5 +76,7 @@ def convert_msstats_differential(
         output_file_prefix=output_prefix_file,
         delete_existing=delete_existing,
     )
-    if generate_project:
-        de_handler.update_project_file(project_file)
+
+cli.add_command(convert_msstats_differential)
+if __name__ == '__main__':
+    cli()