Update docs

docs/source/conf.py

@@ -20,6 +20,8 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 
+import mamotif
+import sphinx_rtd_theme
 
 # -- General configuration ------------------------------------------------
 
@@ -30,9 +32,10 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc',
-    'sphinx.ext.imgmath',
-    'sphinx.ext.viewcode']
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx_rtd_theme'
+]
 
 # Add any paths that contain templates here, relative to this directory.
 # templates_path = ['_templates']
@@ -56,9 +59,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'1.0'
+version = mamotif.__version__
 # The full version, including alpha/beta/rc tags.
-release = u'1.0.1'
+release = mamotif.__version__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -78,7 +81,6 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
-
 # -- Options for HTML output ----------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -95,7 +97,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+# html_static_path = ['_static']
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -112,13 +114,11 @@
     ]
 }
 
-
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'MAmotifdoc'
 
-
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {
@@ -147,7 +147,6 @@
      u'ShaoLab', 'manual'),
 ]
 
-
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
@@ -157,7 +156,6 @@
      [author], 1)
 ]
 
-
 # -- Options for Texinfo output -------------------------------------------
 
 # Grouping the document tree into Texinfo files. List of tuples
@@ -169,5 +167,6 @@
      'Miscellaneous'),
 ]
 
-
-
+linkcheck_ignore = [
+    r"https://github.com/shao-lab/MAmotif/workflows/Python%20package/badge.svg"
+]

docs/source/demo.rst

@@ -3,17 +3,18 @@
 Example Usage
 =============
 
-Here we provide a step-by-step instruction on how to use MAmotif to find candidate cell-type specific regulators
-associated with certain histone modifications.
+Here we provide a step-by-step instruction on how to use MAmotif to find candidate
+cell-type specific regulators associated with certain histone modifications.
 
-We take the H3K4me3 analysis between adult and fetal ProES in MAmotif paper as an example:
+We take the H3K4me3 analysis between adult and fetal ProES in the MAmotif
+paper as an example:
 
 1. Install MAmotif::
 
     $pip install mamotif
     $conda install -c bioconda mamotif
 
-2. Download all data MAmotif needs::
+2. Download example data files::
 
     $mkdir MAmotif_demo
     $cd MAmotif_demo
@@ -23,46 +24,33 @@ We take the H3K4me3 analysis between adult and fetal ProES in MAmotif paper as a
     $wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM908nnn/GSM908039/suppl/GSM908039_H3K4me3-A.bed.gz
     $gzip -d *gz
 
-    Remove the header line and ribosomal reads (You do not need to do this for modern ChIP-seq mapping softwares)
+    Remove the header line and ribosomal reads
     $sed -i '1d' GSM908038_H3K4me3-F.bed
     $sed -i '1d' GSM908039_H3K4me3-A.bed
-    $sed -i '8986927,$d' GSM908039_H3K4me3-F.bed
+    $sed -i '8986927,$d' GSM908038_H3K4me3-F.bed
     $sed -i '14916308,$d' GSM908039_H3K4me3-A.bed
 
-    Substitute space into tab for bed files (You do not need to do this for your own bed files are tab-separated)
+    Substitute space into tab for bed files
     $sed -i "s/ /\t/g" GSM908038_H3K4me3-F.bed
     $sed -i "s/ /\t/g" GSM908039_H3K4me3-A.bed
 
+.. note::
 
-3. Build for genome sequences::
+    The modification steps of data files above is specific to the example,
+    since the format does not follow the standard. You do not have to do this
+    for your own data.
 
-    $mkdir genome
-    $cd genome
-    $wget http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/chromFa.zip
-    $unzip chromFa.zip
-    $cat *fa > hg18.fa
-    $genomecompile -G hg18.fa -o hg18
-    $cd ..
 
-4. Build for motif PWM (Optional)
+3. Install genome `hg18` from UCSC database::
 
-The motif matrix file which containing the motif score cutoff is already packaged under /data directory under MotifScan package.
+    $ motifscan genome --install -n hg18 -r hg18
 
-You can download it by::
+4. Install motif PFMs set from JASPAR database::
 
-    $wget --no-check-certificate https://github.com/shao-lab/MAmotif/raw/master/data/motif.tar.gz
-
-If you want you compile for your custom motifs, please run the following commands::
-
-    $mkdir motif
-    $cd motif
-    $wget http://jaspar2016.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/nonredundant.tar.gz
-    $tar -xzvf nonredundant.tar.gz
-    $motifcompile -M nonredundant/pfm_vertebrates.txt -g ../genome/hg18 -o hg18_jaspar2016_nonredundant_vertebrates
-    $cd ..
+    $ motifscan motif --install -n vertebrates -r vertebrates_non-redundant -g hg19
 
 5. Run MAmotif::
 
-   $mamotif --p1 GSM908039_H3K4me3-A_peaks.bed --p2 GSM908038_H3K4me3-F_peaks.bed --r1 GSM908039_H3K4me3-A.bed --r2 GSM908038_H3K4me3-F.bed -g genome/hg18 -m motif/hg18_jaspar2016_nonredundant_vertebrates_1e-4.txt -o AvsF_H3K4me3_MAmotif
+   $mamotif run --p1 GSM908039_H3K4me3-A_peaks.bed --p2 GSM908038_H3K4me3-F_peaks.bed --r1 GSM908039_H3K4me3-A.bed --r2 GSM908038_H3K4me3-F.bed -g hg18 -m vertebrates -o AvsF_H3K4me3_MAmotif
 
-6. Check the output of MAmotif
+6. Check the output of MAmotif