Added new function text

pgpipe/bed_utilities.py

@@ -19,6 +19,22 @@
     Utilites
     ########
 
+    ***************
+    Windows Utility
+    ***************
+
+    Given a chromosome size file, the windows utility will generate a BED file of 
+    interval features.
+
+    =============
+    Example usage
+    =============
+    Return a BED with interval features that do not extend outside the chromosomes:
+
+    .. code-block:: bash
+        
+        bed_utilities.py --utility windows --chrom-file hg18.chrom.sizes --window-size 1000 --out hg18_windows.bed
+
     **************
     Sample Utility
     **************
@@ -115,6 +131,22 @@
         
         bed_utilities.py --utility complement --bed examples/files/chr1_sites.bed --chrom-file examples/files/chr_sizes.txt
 
+    *****************
+    Intersect Utility
+    *****************
+
+    Given a BED file and an intersect file, return only the interval features within the BED
+    file that overlap with the intersect file. 
+
+    =============
+    Example usage
+    =============
+    Return a BED with only intersecting interval features:
+
+    .. code-block:: bash
+        
+        bed_utilities.py --utility intersect --bed hg18_windows.bed --intersect-file Intersect.vcf.gz --out hg18_intersects.bed
+
     *************
     Merge Utility
     *************
@@ -164,8 +196,8 @@
 
         Appropriate files may be downloaded from the `UCSC Genome Browser <http://hgdownload.soe.ucsc.edu/downloads.html>`_. 
         The supported **ASSEMBLY.chrom.sizes** file for each assembly may be found by 
-        clicking *Genome sequence files and select annotations* (followed by
-        *Standard genome sequence files and select annotations* on select assemblies).
+        clicking **Genome sequence files and select annotations** (followed by
+        **Standard genome sequence files and select annotations** on select assemblies).
     
     #############################
     Output Command-line Arguments
@@ -230,6 +262,14 @@
         Argument used to define the length of base pairs (bp) to extend downstream of 
         features.
 
+    ****************************************
+    Intersect Utility Command-line Arguments
+    ****************************************
+    **--intersect-file** *<intersect_file_filename>*
+        Argument used to define the BED/VCF/VCF.gz file used to remove features that 
+        do not intersect with the given file's features/variants.
+        removing features/positions.
+        
     ************************************
     Merge Utility Command-line Arguments
     ************************************