Merge pull request #159 from lldelisle/moreAutomatisationInREADME

bash script to update the README

Author: bgruening

README.md

@@ -444,6 +444,7 @@ Here is a table to summarize which are the parameters that can be use for each o
 Empty means this parameter is not used.
 not set means that by default the parameter is commented.
 
+<!--- Start of default table -->
 parameter | x-axis | epilogos | links | domains | bed | narrow_peak | bigwig | bedgraph | bedgraph_matrix | hlines | hic_matrix
 -- | - | - | - | - | - | - | - | - | - | - | -
 where | bottom |  |  |  |  |  |  |  |  |  | 
@@ -490,12 +491,12 @@ show_masked_bins |  |  |  |  |  |  |  |  |  |  | false
 scale_factor |  |  |  |  |  |  |  |  |  |  | 1
 transform |  |  |  |  |  |  |  |  |  |  | no
 colormap |  |  |  |  |  |  |  |  |  |  | RdYlBu_r
-
+<!--- End of default table -->
 
 Some parameters can take only discrete values.
 
 They are summarized here:
-
+<!--- Start of possible table -->
 - **where**:
   - for *x-axis*: top, bottom
 - **orientation**:
@@ -542,6 +543,7 @@ They are summarized here:
   - for *bigwig, bedgraph*: true, false
 - **arrowhead_included**:
   - for *bed*: true, false
+<!--- End of possible table -->
 
 Adding new tracks
 -----------------

pygenometracks/updateREADME.sh

@@ -0,0 +1,15 @@
+# This bash script can be used to regenerate the README when parameters changed in tracksclasses.
+
+# Firts run the python script getAllDefaultsAndPossible.py
+python pygenometracks/getAllDefaultsAndPossible.py 
+
+# This generates 2 tables to include in the README
+# First include the first one: docs/content/all_default_properties.txt
+awk 'NR==1,/<!--- Start of default table -->/' README.md > newREADME.md
+cat docs/content/all_default_properties.txt >> newREADME.md
+awk '/<!--- End of default table -->/{toprint = 1}toprint == 1{print}' README.md >> newREADME.md
+# Then include the second one: docs/content/all_possible_properties.txt
+awk 'NR==1,/<!--- Start of possible table -->/' newREADME.md > README.md
+cat docs/content/all_possible_properties.txt >> README.md
+awk '/<!--- End of possible table -->/{toprint = 1}toprint == 1{print}' newREADME.md >> README.md
+rm newREADME.md