Update readme

README.md

@@ -12,16 +12,21 @@ The tool is currently in an **early development stage**.
 COVERnant has several subcommands as its command line help shows:
 
 ```
-$ covernant
-usage: covernant [-h] [--version] {ratio,extract,plot_matrix,bed_to_wig} ...
+$ covernant -h
+usage: covernant [-h] [--version]
+                 {ratio,extract,plot_matrix,bed_to_wig,rescale_wig} ...
 
 positional arguments:
-  {ratio,extract,plot_matrix,bed_to_wig}
+  {ratio,extract,plot_matrix,bed_to_wig,rescale_wig}
                         commands
-    ratio               Generate ratio plots of two alignment files.
-    extract             Extract coverage values from wiggle file.
+    ratio               Generate ratio plots of two alignment files in Bam
+                        formar.
+    extract             Extract coverage values from a wiggle file based on
+                        coordinates in a bed file and generate a matrix.
     plot_matrix         Plot the content of the extracted coverage matrix.
-    bed_to_wig          Converts Bed file to coverage in wiggle formats
+    bed_to_wig          Converts Bed files to coverage files in wiggle formats
+    rescale_wig         Multiplies each value of a wiggle file with a given
+                        factor.
 
 optional arguments:
   -h, --help            show this help message and exit
@@ -31,22 +36,22 @@ optional arguments:
 ## Subcommand `ratio`
 
 ```
-$ covernant ratio -h
-usage: covernant ratio [-h] [--output OUTPUT_PREFIX] [--paired_end]
+usage: covernant ratio [-h] [--denominator DENOMINATOR_BAM_FILE]
+                       [--numerator NUMERATOR_BAM_FILE]
+                       [--output_prefix OUTPUT_PREFIX] [--paired_end]
                        [--window_size WINDOW_SIZE] [--step_size STEP_SIZE]
-                       [--factor FACTOR] [--keep_zero_coverage]
+                       [--factor_numerator FACTOR_NUMERATOR]
+                       [--factor_denominator FACTOR_DENOMINATOR]
+                       [--keep_zero_coverage]
                        [--denominator_name DENOMINATOR_NAME]
                        [--numerator_name NUMERATOR_NAME]
                        [--ratio_name RATIO_NAME]
-                       denominator_bam_file numerator_bam_file
-
-positional arguments:
-  denominator_bam_file
-  numerator_bam_file
 
 optional arguments:
   -h, --help            show this help message and exit
-  --output OUTPUT_PREFIX, -o OUTPUT_PREFIX
+  --denominator DENOMINATOR_BAM_FILE
+  --numerator NUMERATOR_BAM_FILE
+  --output_prefix OUTPUT_PREFIX, -o OUTPUT_PREFIX
   --paired_end          Paired reads are treated as one fragment an the start
                         and end positions are used accordingly
   --window_size WINDOW_SIZE
@@ -55,7 +60,11 @@ optional arguments:
   --step_size STEP_SIZE
                         Step size for sliding window average calculation.
                         Default is 1.
-  --factor FACTOR       A factor the final ratio is multiplied with.
+  --factor_numerator FACTOR_NUMERATOR
+                        A factor the numerator values are are multiplied with.
+  --factor_denominator FACTOR_DENOMINATOR
+                        A factor the denominator values are are multiplied
+                        with.
   --keep_zero_coverage  Also write coordinates that have a coverage of 0.
                         Default is to discard those.
   --denominator_name DENOMINATOR_NAME

README.rst

@@ -0,0 +1,130 @@
+COVERnant
+=========
+
+COVERnant is a tool for the generation and manipulation of coverage
+files (currently in wiggle format) of high-throughput sequencing data.
+
+The tool is currently in an **early development stage**.
+
+COVERnant has several subcommands as its command line help shows:
+
+::
+
+    $ covernant -h
+    usage: covernant [-h] [--version]
+                     {ratio,extract,plot_matrix,bed_to_wig,rescale_wig} ...
+
+    positional arguments:
+      {ratio,extract,plot_matrix,bed_to_wig,rescale_wig}
+                            commands
+        ratio               Generate ratio plots of two alignment files in Bam
+                            formar.
+        extract             Extract coverage values from a wiggle file based on
+                            coordinates in a bed file and generate a matrix.
+        plot_matrix         Plot the content of the extracted coverage matrix.
+        bed_to_wig          Converts Bed files to coverage files in wiggle formats
+        rescale_wig         Multiplies each value of a wiggle file with a given
+                            factor.
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      --version, -v         show version
+
+Subcommand ``ratio``
+--------------------
+
+::
+
+    usage: covernant ratio [-h] [--denominator DENOMINATOR_BAM_FILE]
+                           [--numerator NUMERATOR_BAM_FILE]
+                           [--output_prefix OUTPUT_PREFIX] [--paired_end]
+                           [--window_size WINDOW_SIZE] [--step_size STEP_SIZE]
+                           [--factor_numerator FACTOR_NUMERATOR]
+                           [--factor_denominator FACTOR_DENOMINATOR]
+                           [--keep_zero_coverage]
+                           [--denominator_name DENOMINATOR_NAME]
+                           [--numerator_name NUMERATOR_NAME]
+                           [--ratio_name RATIO_NAME]
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      --denominator DENOMINATOR_BAM_FILE
+      --numerator NUMERATOR_BAM_FILE
+      --output_prefix OUTPUT_PREFIX, -o OUTPUT_PREFIX
+      --paired_end          Paired reads are treated as one fragment an the start
+                            and end positions are used accordingly
+      --window_size WINDOW_SIZE
+                            Window size for sliding window average calculation.
+                            Must be an odd number. (Default is 1).
+      --step_size STEP_SIZE
+                            Step size for sliding window average calculation.
+                            Default is 1.
+      --factor_numerator FACTOR_NUMERATOR
+                            A factor the numerator values are are multiplied with.
+      --factor_denominator FACTOR_DENOMINATOR
+                            A factor the denominator values are are multiplied
+                            with.
+      --keep_zero_coverage  Also write coordinates that have a coverage of 0.
+                            Default is to discard those.
+      --denominator_name DENOMINATOR_NAME
+      --numerator_name NUMERATOR_NAME
+      --ratio_name RATIO_NAME
+
+Subcommand ``extract``
+----------------------
+
+::
+
+    $ covernant extract -h
+    usage: covernant extract [-h] [--output_prefix OUTPUT_PREFIX]
+                             [--flip_reverse_strand]
+                             [--matrix_alignment {left,center,right}]
+                             [--window_size WINDOW_SIZE] [--step_size STEP_SIZE]
+                             coverage_file coordinate_file
+
+    positional arguments:
+      coverage_file
+      coordinate_file
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      --output_prefix OUTPUT_PREFIX
+      --flip_reverse_strand
+                            Flip the coverage value list of entries located at the
+                            minus strand
+      --matrix_alignment {left,center,right}
+                            default is 'left'.
+      --window_size WINDOW_SIZE
+                            Window size for sliding window average calculation.
+                            Must be an odd number.
+      --step_size STEP_SIZE
+                            Step size for sliding window average calculation.
+                            Default is 1.
+
+Subcommand ``plot_matrix``
+--------------------------
+
+::
+
+    $ covernant plot_matrix -h
+    usage: covernant plot_matrix [-h] [--output_file OUTPUT_FILE]
+                                 [--share_x_range] [--share_y_max]
+                                 matrix_file
+
+    positional arguments:
+      matrix_file
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      --output_file OUTPUT_FILE
+      --share_x_range       Use the same x range in all plots.
+      --share_y_max         Use the same maximum y value in all plots.
+
+Subcommand ``bed_to_wig``
+-------------------------
+
+::
+
+    $ covernant bed_to_wig -h
+    usage: covernant bed_to_wig [-h] [--output_prefix OUTPUT_PREFIX]
+                                [--window_size WINDOW_SIZE]