modisco (#22)

* modisco added

* modisco slow version

* io

* add modisco-lite to setup dependencies

* bug fix in bigwig writer

* update doc and warning

* cli fix

---------

Co-authored-by: Muhammed Hasan Celik <celik.muhammed_hasan@gene.com>

Author: MuhammedHasan

setup.cfg

@@ -70,6 +70,7 @@ install_requires =
     pyBigWig
     pyarrow
     tangermeme
+    modisco-lite
 
 [options.packages.find]
 where = src

src/decima/cli/__init__.py

@@ -8,6 +8,7 @@
 from decima.cli.vep import cli_predict_variant_effect
 from decima.cli.finetune import cli_finetune
 from decima.cli.vep import cli_vep_ensemble
+from decima.cli.modisco import cli_modisco_attributions, cli_modisco_patterns, cli_modisco_reports, cli_modisco
 
 
 logger = logging.getLogger("decima")
@@ -35,6 +36,10 @@ def main():
 main.add_command(cli_predict_variant_effect, name="vep")
 main.add_command(cli_finetune, name="finetune")
 main.add_command(cli_vep_ensemble, name="vep-ensemble")
+main.add_command(cli_modisco_attributions, name="modisco-attributions")
+main.add_command(cli_modisco_patterns, name="modisco-patterns")
+main.add_command(cli_modisco_reports, name="modisco-reports")
+main.add_command(cli_modisco, name="modisco")
 
 
 if __name__ == "__main__":