Merge pull request #152 from lldelisle/updated_doc

updated readme with last parameters and changed file location

Author: bgruening

README.md

@@ -469,6 +469,8 @@ global_max_row |  |  |  |  | false |  |  |  |  |  |
 gene_rows |  |  |  |  | not set |  |  |  |  |  | 
 arrow_interval |  |  |  |  | 2 |  |  |  |  |  | 
 arrowhead_included |  |  |  |  | false |  |  |  |  |  | 
+color_utr |  |  |  |  | grey |  |  |  |  |  | 
+height_utr |  |  |  |  | 1 |  |  |  |  |  | 
 show_data_range |  |  |  |  |  | true | true | true | true | true | 
 show_labels |  |  |  |  |  | true |  |  |  |  | 
 use_summit |  |  |  |  |  | true |  |  |  |  | 

all_default_properties.txt renamed to docs/content/all_default_properties.txt

@@ -23,6 +23,8 @@ global_max_row |  |  |  |  | false |  |  |  |  |  |
 gene_rows |  |  |  |  | not set |  |  |  |  |  | 
 arrow_interval |  |  |  |  | 2 |  |  |  |  |  | 
 arrowhead_included |  |  |  |  | false |  |  |  |  |  | 
+color_utr |  |  |  |  | grey |  |  |  |  |  | 
+height_utr |  |  |  |  | 1 |  |  |  |  |  | 
 show_data_range |  |  |  |  |  | true | true | true | true | true | 
 show_labels |  |  |  |  |  | true |  |  |  |  | 
 use_summit |  |  |  |  |  | true |  |  |  |  | 

all_possible_properties.txt renamed to docs/content/all_possible_properties.txt

@@ -1,14 +1,15 @@
 """
 This python script will generate two files:
-- all_default_properties.txt
+- docs/content/all_default_properties.txt
 This file is a markdown table with all the defaults values for each parameter
 for each track class. This table can be copy pasted in the README.md
-- all_possible_properties.txt
+- docs/content/all_possible_properties.txt
 This file is a markdown list with possible values.
 This can also be copy pasted in the README.md
 """
 from pygenometracks.tracksClass import PlotTracks, XAxisTrack
 import numpy as np
+import os.path
 
 not_used_string = ''
 not_set_string = 'not set'
@@ -98,10 +99,12 @@ def main():
 
             mat[i + 2, j] = default
     # The matrix is written in a file to be able to use it in the README.md
-    np.savetxt("all_default_properties.txt", mat, fmt='%s', delimiter=" | ")
+    np.savetxt(os.path.join("docs", "content", "all_default_properties.txt"),
+               mat, fmt='%s', delimiter=" | ")
 
     # For the possible:
-    with open("all_possible_properties.txt", 'w') as fo:
+    with open(os.path.join("docs", "content", "all_possible_properties.txt"),
+              'w') as fo:
         for p, possible_dic in all_possible_parameters.items():
             possible_values = {}
             for track_type, pv in possible_dic.items():