add command line usage documentation

.gitlab-ci.yml

@@ -13,7 +13,7 @@ pages:
     - pip3 install sphinx
     - yum install -y make
     - pip3 install sphinx
-    - pip3 install sphinxcontrib-bibtex
+    - pip3 install sphinxcontrib-bibtex sphinx_rtd_theme sphinx-argparse
     - pip3 install -r impute_jass/requirements.txt
     - cd impute_jass/doc
     - make html
@@ -22,4 +22,4 @@ pages:
     paths:
     - public
   only:
-  - master
\ No newline at end of file
+  - master

impute_jass/doc/source/conf.py

@@ -46,7 +46,8 @@ extensions = [
     'sphinx.ext.mathjax',
     'sphinx.ext.viewcode',
     'sphinx.ext.autosummary',
-    'sphinxcontrib.bibtex'
+    'sphinxcontrib.bibtex',
+    'sphinxarg.ext'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -82,7 +83,7 @@ pygments_style = 'sphinx'
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'bizstyle'
+html_theme = 'sphinx_rtd_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

impute_jass/doc/source/index.rst

@@ -4,7 +4,7 @@
    contain the root `toctree` directive.
 
 Welcome to the Robust and Accurate Imputation from Summary Statistics (RAISS) documentation!
-=====================================
+============================================================================================
 
 .. toctree::
    :maxdepth: 2
@@ -13,8 +13,8 @@ Welcome to the Robust and Accurate Imputation from Summary Statistics (RAISS) do
 What is RAISS ?
 ===================
 
-RAISS is python package to impute missing SNP summary statistics from
-neighborring SNPs in linkage desiquilibrium.
+RAISS is a python package to impute missing SNP summary statistics from
+neighboring SNPs in linkage desiquilibrium.
 
 The statistical model used to make the imputation is described in :cite:`Pasaniuc2014`
 
@@ -35,15 +35,16 @@ Installation
 Precomputation of LD-correlation
 =================================
 
-The imputation is based the Linkage desiquilibrium between SNPs.
+The imputation is based the Linkage desiquilibrium
+between SNPs.
 
-To save computation the LD is computed and saved perform the imputation is
-performed. To limit the number of SNP pairs, the LD is computed between pairs of
+To save computation time, the LD is computed before imputation and saved as tabular format.
+To limit the number of SNP pairs, the LD is computed between pairs of
 SNPs in a approximately LD-independent regions. For an european ancestry, you can use
 the region defined by :cite:`Berisa2015` that are provided in the package data folder.
 
 To compute the LD you need to specify a reference panel splitted by chromosomes
-(bed, fam and bim formats of plink, see `PLINK formats <https://www.cog-genomics.org/plink2/formats>` )
+(bed, fam and bim formats of plink, see `PLINK formats <https://www.cog-genomics.org/plink2/formats>`_ )
 
 
 .. code-block:: python
@@ -59,7 +60,6 @@ To compute the LD you need to specify a reference panel splitted by chromosomes
 Input format:
 =============
 
-
 GWAS results files must be provided in the tabular format by chromosome (tab separated)
 all in the same folder with the following columns with the same header:
 
@@ -69,13 +69,13 @@ all in the same folder with the following columns with the same header:
 | rs6548219| 30762 | A	  | G   | -1.133 |
 +----------+-------+------+-----+--------+
 
-This format can be obtain with the `JASS PreProcessing package <https://gitlab.pasteur.fr/statistical-genetics/JASS_Pre-processing>`.
+This format can be obtained with the `JASS PreProcessing package <https://gitlab.pasteur.fr/statistical-genetics/JASS_Pre-processing>`.
 
 
 Launching imputation on one chromosome
 ======================================
 
-RAISS has an interface with the command line.
+RAISS has an interface with the command line (see Command Line Usage bellow).
 
 If you have access to a cluster, an efficient way to use RAISS is to launch
 the imputation of each chromosome on a separate cluster node. The script
@@ -88,6 +88,7 @@ Output
 
 The raiss package outputs imputed GWAS files in the tabular format:
 #TODO suppress complementary columns
+
 +------------+---+--+----------------+-----+-----+----------------+------------------+---------+---------+
 |            |A0 |A1| Nsnp_to_impute |Var  |Z    |condition_number|correct_inversion |ld_score |   pos   |
 +============+===+==+================+=====+=====+================+==================+=========+=========+
@@ -96,18 +97,25 @@ The raiss package outputs imputed GWAS files in the tabular format:
 
 # Keep only useful columns
 
+Command Line Usage
+==================
+
+.. argparse::
+  :ref: impute_jass.__main__.add_chromosome_imputation_argument
 
 Indices and tables
 ==================
 
 * :ref:`genindex`
 * :ref:`modindex`
-* :ref:`search`
-
 .. automodule:: impute_jass
    :members:
+* :ref:`search`
+
+
 
 .. autosummary::
    :toctree: _autosummary
 
+
 .. bibliography:: reference.bib

impute_jass/impute_jass/__main__.py

@@ -32,7 +32,9 @@ def launch_chromosome_imputation(args):
     imputed_zscore.to_csv(z_fo, sep='\t')
     print("Save imputation done at {0}".format(z_fo))
 
-def add_chromosome_imputation_argument(parser):
+def add_chromosome_imputation_argument():
+    
+    parser = argparse.ArgumentParser()
     parser.add_argument('--chrom', required=True, help= "chromosome to impute to the chr\d+ format")
     parser.add_argument('--gwas', required=True, help= "GWAS to impute to the consortia_trait format")
 
@@ -50,7 +52,7 @@ def add_chromosome_imputation_argument(parser):
 
 def main():
 
-    parser = argparse.ArgumentParser()#prog='impute_jass')
+#prog='impute_jass')
     parser = add_chromosome_imputation_argument(parser)
     args = parser.parse_args()
     args.func(args)

impute_jass/setup.py

@@ -9,6 +9,7 @@ setup(name='impute_jass',
       license='MIT',
       #package_dir = {'': 'jass_preprocessing'},
       packages= ['impute_jass'],
+
       package_data = {'impute_jass':'./data/*.csv'},
       zip_safe=False,