Add example usage for docs

docs/source/demo.rst

@@ -0,0 +1,64 @@
+.. _demo:
+
+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.
+
+We take the H3K4me3 analysis between adult and fetal ProES in MAmotif paper as an example:
+
+1. Install MAmotif::
+
+    $pip install mamotif
+    $conda install -c bioconda mamotif
+
+2. Download all data MAmotif needs::
+
+    $mkdir MAmotif_demo
+    $cd MAmotif_demo
+    $wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM908nnn/GSM908038/suppl/GSM908038_H3K4me3-F_peaks.bed.gz
+    $wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM908nnn/GSM908039/suppl/GSM908039_H3K4me3-A_peaks.bed.gz
+    $wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM908nnn/GSM908038/suppl/GSM908038_H3K4me3-F.bed.gz
+    $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)
+    $sed -i '1d' GSM908038_H3K4me3-F.bed
+    $sed -i '1d' GSM908039_H3K4me3-A.bed
+    $sed -i '8986927,$d' GSM908039_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)
+    $sed -i "s/ /\t/g" GSM908038_H3K4me3-F.bed
+    $sed -i "s/ /\t/g" GSM908039_H3K4me3-A.bed
+
+
+3. Build for genome sequences::
+
+    $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)
+
+The motif matrix file which containing the motif score cutoff is already packaged under /data directory under MotifScan package.
+
+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 ..
+
+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
+
+6. Check the output of MAmotif

docs/source/index.rst

@@ -33,6 +33,7 @@ Contents
 
    intro
    tutorial
+   demo
    changelog
    faq
    license