add cite subcommand

.github/workflows/pydamage_ci.yml

@@ -36,4 +36,6 @@ jobs:
       - name: Check pydamage on test data
         shell: bash -l {0}
         run: |
-          pydamage analyze --verbose tests/data/aligned.bam
+          pydamage analyze --verbose tests/data/aligned.bam
+          pydamage filter pydamage_results/pydamage_results.csv
+          pydamage cite

pydamage/citation.py

@@ -0,0 +1,15 @@
+def get_citation():
+    BIB = """
+@article{Borry2021_pydamage,
+author = {Borry, Maxime and Huebner, Alexander and Rohrlach, Adam B and Warinner, Christina G},
+doi = {10.1101/2021.03.24.436838},
+elocation-id = {2021.03.24.436838},
+eprint = {https://www.biorxiv.org/content/early/2021/03/24/2021.03.24.436838.full.pdf},
+journal = {bioRxiv},
+publisher = {Cold Spring Harbor Laboratory},
+title = {PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly},
+url = {https://www.biorxiv.org/content/early/2021/03/24/2021.03.24.436838},
+year = {2021}
+}
+"""
+    print(BIB)

pydamage/cli.py

@@ -2,11 +2,26 @@
 
 import click
 from pydamage.main import pydamage_analyze
+from pydamage.citation import get_citation
 from pydamage.kneedle import apply_filter
 from pydamage import __version__
+from collections import OrderedDict
 
+class NaturalOrderGroup(click.Group):
 
-@click.group()
+    def __init__(self, name=None, commands=None, **attrs):
+        super(NaturalOrderGroup, self).__init__(
+            name=name, commands=None, **attrs)
+        if commands is None:
+            commands = OrderedDict()
+        elif not isinstance(commands, OrderedDict):
+            commands = OrderedDict(commands)
+        self.commands = commands
+
+    def list_commands(self, ctx):
+        return self.commands.keys()
+
+@click.group(cls=NaturalOrderGroup)
 @click.version_option(__version__)
 @click.pass_context
 @click.option(
@@ -88,6 +103,11 @@ def filter(ctx, no_args_is_help=True, **kwargs):
 
     apply_filter(**kwargs, **ctx.obj)
 
+@cli.command()
+def cite():
+    """Get pydamage citation in bibtex format
+    """
+    get_citation()
 
 if __name__ == "__main__":
     cli()