feat: Adding functionality to the complexity command (#4)

Co-authored-by: Melissa Gymrek <[email protected]>
Co-authored-by: Melissa Gymrek <[email protected]>
Co-authored-by: Arya Massarat <[email protected]>

docs/commands/complexity.rst

@@ -6,24 +6,45 @@ complexity
 
 Compute the complexity of a pangenome graph.
 
-The ``complexity`` command outputs a single float to ``stdout``.
+The ``complexity`` command outputs a file with complexity metrics for an entire graph or for a specified set of regions from a graph.
+
+If a GFA file is provided, the whole graph is processed.
+
+If a GBZ file is provided, you must specify a region or list of regions to process.
 
 Usage
 ~~~~~
 .. code-block:: bash
 
   panct complexity \
-  --verbosity [CRITICAL|ERROR|WARNING|INFO|DEBUG|NOTSET] \
-  GFA
+    --gfa GFAFILE \
+    --out OUTFILE
+    --verbosity [CRITICAL|ERROR|WARNING|INFO|DEBUG|NOTSET]
 
 Examples
 ~~~~~~~~
 .. code-block:: bash
 
-  panct complexity tests/data/basic.gfa
+  panct complexity --gfa tests/data/test.gfa --out test.tab
 
 All files used in these examples are described :doc:`here </project_info/example_files>`.
 
+Additional examples
+~~~~~~~~~~~~~~~~~~~
+
+Below are additional examples based on the HPRC .gbz format graph (not included in this repo but available `here <https://github.com/human-pangenomics/hpp_pangenome_resources>`_). 
+
+.. code-block:: bash
+
+  # Run on a single region
+  panct complexity --gbz hprc-v1.1-mc-grch38.gbz \
+    --region chr11:119077050-119178859 --out test.tab \
+    --metrics sequniq-normwalk,sequniq-normnode
+
+  # Run on a file with a list of regions
+  panct complexity --gbz hprc-v1.1-mc-grch38.gbz \
+    --region regions.bed --out test.tab \
+    --metrics sequniq-normwalk,sequniq-normnode
 
 Detailed Usage
 ~~~~~~~~~~~~~~

example-analysis/example.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+# Get complexity for an example region
+panct complexity \
+	--region chr11:119077050-119178859 --out test.tab \
+	--metrics sequniq-normwalk,sequniq-normnode \
+	../testdata/hprc-v1.1-mc-grch38.gbz
+
+# Make windows across hg38
+bedtools makewindows -g hg38.txt -w 100000 > hg38_windows_100kb.bed
+
+# Get complexity for each window
+panct complexity \
+	--region-file hg38_windows_100kb.bed --out hg38_100kb.tab \
+	--metrics sequniq-normwalk,sequniq-normnode \
+	../testdata/hprc-v1.1-mc-grch38.gbz
+
+# Test out for list of GWAS hits
+panct complexity \
+	--region-file trubetskoy_scz_hg38.bed --out hg38_100kb_trubetskoy.tab \
+	--metrics sequniq-normwalk,sequniq-normnode \
+	../testdata/hprc-v1.1-mc-grch38.gbz

example-analysis/hg38.txt

@@ -0,0 +1,25 @@
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example-analysis/trubetskoy_scz_hg38.bed

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