Merge pull request #120 from maxplanck-ie/docu_update

changes in help messages
deeptools · Sep 8, 2017 · 3ad8f8b · 3ad8f8b
2 parents e4d13ef + ad13929
commit 3ad8f8b
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Showing 3 changed files with 25 additions and 10 deletions.
diff --git a/hicexplorer/hicExport.py b/hicexplorer/hicExport.py
@@ -23,9 +23,12 @@ def parse_arguments(args=None):
                         required=True)
 
     parser.add_argument('--inputFormat',
-                        help='file format for input file. \n'
-                             '(options : hicexplorer, lieberman, npz (file format of previous hicexplorer versions),'
-                             'dekker.',
+                        help='file format for the matrix file. \n'
+                             'The following options are available: `hicexplorer` (native HiCExplorer format, '
+                             '`npz` (format used by earlier versions of HiCExplorer), '
+                             '`dekker` (matrix format used in Job Dekker publications), '
+                             'and `lieberman` (format used by Erez Lieberman Aiden). This last formats may change '
+                             'in the future.',
                         default='hicexplorer')
 
     parser.add_argument('--chrNameList',
@@ -64,7 +67,7 @@ def parse_arguments(args=None):
                              'The "ren" format is a list of tuples of the form '
                              'chrom, bin_star, bin_end, values. '
                              'The lieberman format writes separate files for each chromosome,'
-                             'with three columns : contact start, contact end, and raw observed score. '
+                             'with three columns: contact start, contact end, and raw observed score. '
                              'This corresponds to the RawObserved files from lieberman group. The '
                              'hicexplorer format stores the data using a hdf5 format. Optionally, '
                              'the numpy npz format can be used for small datasets (< 4GB).'

diff --git a/hicexplorer/hicFindTADs.py b/hicexplorer/hicFindTADs.py
@@ -42,7 +42,7 @@ def parse_arguments(args=None):
 are used to call the TADs. This is convenient to test different filtering criteria quickly
 as the demanding step is the computation of TAD-separation scores.
 
- An simple example usage is:
+ A simple example usage is:
 
 $ hicFindTads -m hic_matrix.h5 --outPrefix TADs
 

diff --git a/hicexplorer/hicInfo.py b/hicexplorer/hicInfo.py
@@ -5,13 +5,25 @@
 
 def parse_arguments(args=None):
 
-    parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter,
-                                     description=('Prints information about a matrix including size, '
-                                                  'number of elements, sum of elements, etc.'))
+    parser = argparse.ArgumentParser(
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        description="""
+Prints information about a matrix or matrices including matrix size,
+number of elements, sum of elements, etc.
+
+An example usage is:
+
+$ hicInfo -m matrix1.h5 matrix2.h5 matrix3.h5
+
+""")
 
     parser.add_argument('--matrices', '-m',
-                        help='The matrix (matrices) to get information about.',
-                        metavar='HiCExplorer supports: h5, npz, dekker and lieberman file format.',
+                        help='The matrix (or multiple matrices) to get information about. '
+                             'HiCExplorer supports the following file formats: h5 (native HiCExplorer format), '
+                             'npz (format used by earlier versions of HiCExplorer), '
+                             'dekker (matrix format used in Job Dekker publications), '
+                             'and lieberman (format used by Erez Lieberman Aiden). This last formats may change '
+                             'in the future.',
                         nargs='+',
                         required=True)