Merge branch 'dev'

README.mkd

@@ -4,7 +4,7 @@
 
 # genipe - A Python module to perform genome-wide imputation analysis
 
-*Version 1.2.1*
+*Version 1.2.2*
 
 The `genipe` module (standing for **GEN**ome-wide **I**mputation
 **P**ipelin**E**) includes a script (named `genipe-launcher`) that
@@ -40,7 +40,7 @@ The tool requires a standard [Python](http://python.org/) 3 installation with
 the following modules:
 
 * `numpy` version 1.8.2 and latest
-* `jinja2` version 2.7.3 and latest
+* `Jinja2` version 2.7.3 and latest
 * `pandas` version 0.15.2 and latest
 * `setuptools` version 12.0.5 and latest
 
@@ -103,9 +103,10 @@ usage: genipe-launcher [-h] [-v] [--debug] [--thread THREAD] --bfile PREFIX
                        [--probability FLOAT] [--completion FLOAT]
                        [--info FLOAT] [--report-number NB]
                        [--report-title TITLE] [--report-author AUTHOR]
+                       [--report-background BACKGROUND]
 
 Execute the genome-wide imputation pipeline. This script is part of the
-'genipe' package, version 1.2.1.
+'genipe' package, version 1.2.2.
 
 optional arguments:
   -h, --help            show this help message and exit
@@ -174,6 +175,10 @@ Automatic Report Options:
                         imputation]
   --report-author AUTHOR
                         The report author. [Automatically generated by genipe]
+  --report-background BACKGROUND
+                        The report background section (can either be a string
+                        or a file containing the background. [General
+                        background]
 ```
 
 
@@ -212,7 +217,7 @@ usage: imputed-stats [-h] [-v] {cox,linear,logistic,mixedlm,skat} ...
 
 Performs statistical analysis on imputed data (either SKAT analysis, or
 linear, logistic or survival regression). This script is part of the 'genipe'
-package, version 1.2.1).
+package, version 1.2.2).
 
 optional arguments:
   -h, --help            show this help message and exit

docs/conf.py

@@ -295,6 +295,6 @@
 intersphinx_mapping = {
     'https://docs.python.org/3.4': None,
     'numpy': ('http://docs.scipy.org/doc/numpy/', None),
-    'pandas': ('http://pandas.pydata.org/pandas-docs/dev', None),
+    'pandas': ('http://pandas.pydata.org/pandas-docs/stable/', None),
     'jinja2': ('http://jinja.pocoo.org/docs', None),
 }

docs/index.rst

@@ -55,9 +55,10 @@ Usage
                           [--probability FLOAT] [--completion FLOAT]
                           [--info FLOAT] [--report-number NB]
                           [--report-title TITLE] [--report-author AUTHOR]
+                          [--report-background BACKGROUND]
 
    Execute the genome-wide imputation pipeline. This script is part of the
-   'genipe' package, version 1.2.1.
+   'genipe' package, version 1.2.2.
 
    optional arguments:
      -h, --help            show this help message and exit
@@ -126,6 +127,10 @@ Usage
                            imputation]
      --report-author AUTHOR
                            The report author. [Automatically generated by genipe]
+     --report-background BACKGROUND
+                           The report background section (can either be a string
+                           or a file containing the background. [General
+                           background]
 
 
 About

docs/tutorials/tutorial_SKAT.rst

@@ -9,6 +9,7 @@ Quick navigation
 3. :ref:`skat-tut-3`
 4. :ref:`skat-tut-4`
 5. :ref:`skat-tut-5`
+6. :ref:`skat-tut-6`
 
 SKAT analysis tutorial
 -----------------------
@@ -130,6 +131,7 @@ thresholds.
 Only the variants in this file will be considered by the ``imputed-stats``
 tool.
 
+
 .. _skat-tut-2:
 
 Creating a SNP sets file
@@ -189,6 +191,7 @@ variants. If you want to use custom weights based on something la
 deleteriousness prediction, you need to generate the weights manually and
 provide them in the SNP set file as shown here.
 
+
 .. _skat-tut-3:
 
 Format for the phenotypes file
@@ -220,6 +223,7 @@ file, as well as covariates. The covariates are included in the analysis using
 the ``--covar`` argument and the variable type of the outcome is given using
 the ``--outcome-type`` argument which can be set to `discrete` or `continuous`.
 
+
 .. _skat-tut-4:
 
 Running the script
@@ -282,6 +286,7 @@ The line by line explanation of this command is as follows:
     Also note that the SKAT-O algorithm can be used by using the ``--skat-o``
     flag.
 
+
 .. _skat-tut-5:
 
 Results
@@ -314,3 +319,85 @@ If you have any questions or problems, don't hesitate to contact us through our
 
 We are also very open to suggestions and improvements. If you have developed a
 new interesting feature, please send us a push request from Github.
+
+
+.. _skat-tut-6:
+
+Usage
+^^^^^^
+
+The following command will display the documentation for the SKAT analysis in
+the console:
+
+.. code-block:: console
+
+   $ imputed-stats skat --help
+   usage: imputed-stats skat [-h] [-v] [--debug] --impute2 FILE --sample FILE
+                             --pheno FILE [--extract-sites FILE] [--out FILE]
+                             [--nb-process INT] [--nb-lines INT] [--chrx]
+                             [--gender-column NAME] [--scale INT] [--prob FLOAT]
+                             [--maf FLOAT] [--covar NAME] [--categorical NAME]
+                             [--missing-value NAME] [--sample-column NAME]
+                             [--interaction NAME] --snp-sets FILE --outcome-type
+                             {continuous,discrete} [--skat-o] --pheno-name NAME
+
+   Uses the SKAT R package to analyze user defined gene sets. This script is part
+   of the 'genipe' package, version 1.2.2).
+
+   optional arguments:
+     -h, --help            show this help message and exit
+     -v, --version         show program's version number and exit
+     --debug               set the logging level to debug
+
+   Input Files:
+     --impute2 FILE        The output from IMPUTE2.
+     --sample FILE         The sample file (the order should be the same as in
+                           the IMPUTE2 files).
+     --pheno FILE          The file containing phenotypes and co variables.
+     --extract-sites FILE  A list of sites to extract for analysis (optional).
+
+   Output Options:
+     --out FILE            The prefix for the output files. [imputed_stats]
+
+   General Options:
+     --nb-process INT      The number of process to use. [1]
+     --nb-lines INT        The number of line to read at a time. [1000]
+     --chrx                The analysis is performed for the non pseudo-autosomal
+                           region of the chromosome X (male dosage will be
+                           divided by 2 to get values [0, 0.5] instead of [0, 1])
+                           (males are coded as 1 and option '--gender-column'
+                           should be used).
+     --gender-column NAME  The name of the gender column (use to exclude samples
+                           with unknown gender (i.e. not 1, male, or 2, female).
+                           If gender not available, use 'None'. [Gender]
+
+   Dosage Options:
+     --scale INT           Scale dosage so that values are in [0, n] (possible
+                           values are 1 (no scaling) or 2). [2]
+     --prob FLOAT          The minimal probability for which a genotype should be
+                           considered. [>=0.9]
+     --maf FLOAT           Minor allele frequency threshold for which marker will
+                           be skipped. [<0.01]
+
+   Phenotype Options:
+     --covar NAME          The co variable names (in the phenotype file),
+                           separated by coma.
+     --categorical NAME    The name of the variables that are categorical (note
+                           that the gender is always categorical). The variables
+                           are separated by coma.
+     --missing-value NAME  The missing value in the phenotype file.
+     --sample-column NAME  The name of the sample ID column (in the phenotype
+                           file). [sample_id]
+     --interaction NAME    Add an interaction between the genotype and this
+                           variable.
+
+   SKAT Options:
+     --snp-sets FILE       A file indicating a snp_set and an optional weight for
+                           every variant.
+     --outcome-type {continuous,discrete}
+                           The variable type for the outcome. This will be passed
+                           to SKAT.
+     --skat-o              By default, the regular SKAT is used. Setting this
+                           flag will use the SKAT-O algorithm instead.
+     --pheno-name NAME     The phenotype.
+

docs/tutorials/tutorial_cox.rst

@@ -233,7 +233,7 @@ in the console:
                             NAME
 
    Performs a survival regression on imputed data using Cox's proportional hazard
-   model. This script is part of the 'genipe' package, version 1.2.1).
+   model. This script is part of the 'genipe' package, version 1.2.2).
 
    optional arguments:
      -h, --help            show this help message and exit

docs/tutorials/tutorial_extract.rst

@@ -172,6 +172,12 @@ The following example shows two lines of the ``.impute2`` file.
    22 rs7289830 16058758 C A 0 0 1 0 0 1 0 1 0 ...
    22 rs6423472 16087621 A G 0 1 0 1 0 0 0 1 0 ...
 
+.. note::
+
+   When extracting using the ``impute2`` format, all the existing companion
+   files (``.maf``, ``.map``, etc.) will also be extracted and included in the
+   same directory (using the same output prefix).
+
 
 ``.dosage`` file
 """""""""""""""""
@@ -239,7 +245,7 @@ analysis in the console:
                             [--rate FLOAT] [--info FLOAT]
 
    Extract imputed markers located in a specific genomic region. This script is
-   part of the 'genipe' package, version 1.2.1).
+   part of the 'genipe' package, version 1.2.2).
 
    optional arguments:
      -h, --help            show this help message and exit
@@ -277,3 +283,8 @@ analysis in the console:
                            the specified threshold. Can be use in combination
                            with '--maf', '--rate' and '--genomic'.
 
+.. note::
+
+   When using the ``--index`` option, only the indexation (of files without an
+   index) will be performed.
+

docs/tutorials/tutorial_genipe.rst

@@ -352,8 +352,8 @@ genome-wide imputation of the *HapMap* CEU dataset.
    ``--impute2-bin`` and/or the ``--plink-bin`` options if the SHAPEIT, IMPUTE2
    and/or the Plink binaries are in  the ``PATH`` variable.
 
-The following table describes the option used by :py:mod:`genipe` in the
-previous command (see the :ref:`genipe-usage` section for a full list):
+The following table describes the options **used by** :py:mod:`genipe` **in the
+previous command** (see the :ref:`genipe-usage` section for a full list):
 
 .. table::
 
@@ -411,6 +411,12 @@ previous command (see the :ref:`genipe-usage` section for a full list):
    subsequent steps).
 
 
+.. note::
+
+   Four options will modify the report content: ``--report-number``,
+   ``--report-title``, ``--report-author`` and ``--report-background``.
+
+
 .. _genipe-tut-compile-report:
 
 Compiling the report

docs/tutorials/tutorial_linear.rst

@@ -245,7 +245,7 @@ analysis in the console:
                                --pheno-name NAME
 
    Performs a linear regression (ordinary least squares) on imputed data. This
-   script is part of the 'genipe' package, version 1.2.1).
+   script is part of the 'genipe' package, version 1.2.2).
 
    optional arguments:
      -h, --help            show this help message and exit

docs/tutorials/tutorial_logistic.rst

@@ -236,7 +236,7 @@ regression analysis in the console:
                                  --pheno-name NAME
 
    Performs a logistic regression on imputed data using a GLM with a binomial
-   distribution. This script is part of the 'genipe' package, version 1.2.1).
+   distribution. This script is part of the 'genipe' package, version 1.2.2).
 
    optional arguments:
      -h, --help            show this help message and exit

docs/tutorials/tutorial_mixedlm.rst

@@ -255,7 +255,7 @@ effects analysis in the console:
 
    Performs a linear mixed effects regression on imputed data using a random
    intercept for each group. This script is part of the 'genipe' package, version
-   1.2.1).
+   1.2.2).
 
    optional arguments:
      -h, --help            show this help message and exit

genipe/__init__.py

@@ -19,7 +19,7 @@
 __license__ = "CC BY-NC 4.0"
 __maintainer__ = "Louis-Philippe Lemieux Perreault"
 __email__ = "[email protected]"
-__status__ = "Development"
+__status__ = "Production"
 
 
 chromosomes = range(1, 23)