Merge pull request #75 from jeffreyywangg/Documentation-Enhancements

Fix Issue #67 + Documentation Enhancements

README.md

@@ -19,7 +19,7 @@ To see how to run dcHiC, read our docs and try our demo (below)! Information abo
 
 ### Demo
 
-This README contains the key information you will need to use this application. However, some users may find a demo helpful—ours includes a script to run package installation as well as detailed guides for different options of dcHiC. All of these resources are available in `packages/dchic_demo.zip`, with relevant instructions inside! 
+This README contains the key information you will need to use this application. However, some users may find a demo helpful; ours includes a script to run package installation as well as detailed guides for different options of dcHiC. All of these resources are available in the `demo` directory, with relevant instructions inside! 
 
 ## Installation
 

demo/README.md

@@ -0,0 +1,18 @@
+## Information
+
+The .zip file has a demo directory to test dcHiC. As a
+testing example, principal component (PC) values for
+mouse ESC (4 replicates), NPC (3 replicates) and CN
+(5 replicates) are provided in the **ESC_NPC_CN_100Kb** directory. 
+
+We are also providing demo files to recreate the
+results for pseudo-bulk single cell 3D genome. For testing,
+we are providing the **mouse_cortex_single_cell3D** and
+**mouse_hippocampus_single_cell3D** directories with the required
+files and the expected results folder. The same directories
+contain the `run_dchic.sh` script to recreate the results.
+
+The scripts directory contains the basic but necessary
+scripts to reproduce the results while packages directory
+contains the accessory programs that needs to be installed
+before the dcHiC run.

utility/preprocess.py

@@ -23,7 +23,7 @@
 
 parser.add_argument("-genomeFile", action = "store", dest = "genomeSize", help = "[.cool only] Location of chromosome size file (Must be: hg38, hg19, mm10, mm9)")
 
-parser.add_argument("-removeChr", action = 'store', dest = 'remove', help = "[.hic only] Remove chromosomes: {Chr,Chr,Chr} format. Commonly used for Y. Default MT removed.")
+parser.add_argument("-removeChr", action = 'store', dest = 'remove', help = "[.hic only] Remove chromosomes: {Chr,Chr,Chr} format. Commonly used for Y (default MT). Specify like 'chry' or 'chrY'.")
 
 results = parser.parse_args()
 
@@ -128,7 +128,7 @@
             else:
                 print(f"  - {chrom.name}")
         else:
-            chrTag = "chr" + chrom.name
+            chrTag = "chr" + chrom.name if "chr" not in chrom.name else chrom.name
             chrSize = chrom.length
             chrSizes[chrTag] = chrSize
             chrs.append(chrTag)