create textual output (#343)

* create textual output

* test_cli_resclust.py lint

* Filename matching issue

* test_cli_resclust.py lint

* Update cli_resclust.py lint

src/arctic3d/cli_resclust.py

@@ -23,6 +23,8 @@
     `linkage` : the linkage strategy.
 
     `criterion` : the criterion to extract the clusters.
+
+    `output` : the path where to output clusters data.
 """
 import argparse
 import sys
@@ -36,6 +38,7 @@
     get_clustering_dict,
 )
 from arctic3d.modules.input import Input
+from arctic3d.modules.output import create_output_folder
 
 
 argument_parser = argparse.ArgumentParser()
@@ -88,6 +91,13 @@
     "--chain", help="Segment ID to be considered", required=False
 )
 
+argument_parser.add_argument(
+    "--output",
+    help="Path to the generated output dictionary",
+    type=str,
+    required=False,
+)
+
 
 def load_args(arguments):
     """
@@ -128,7 +138,15 @@ def maincli():
     cli(argument_parser, main)
 
 
-def main(input_arg, residue_list, chain, threshold, linkage, criterion):
+def main(
+    input_arg,
+    residue_list,
+    chain,
+    threshold,
+    linkage,
+    criterion,
+    output,
+):
     """Main function."""
     log.setLevel("INFO")
 
@@ -192,14 +210,32 @@ def main(input_arg, residue_list, chain, threshold, linkage, criterion):
         )
 
         cl_dict = get_clustering_dict(clusters, unique_sorted_resids)
-        for el in cl_dict.keys():
-            log.info(
-                f"cluster {el}, residues"
-                f" {' '.join([str(res) for res in cl_dict[el]])}"
-            )
     else:
         log.info("Only one residue, no clustering performed.")
-        log.info(f"cluster 1, residues {unique_sorted_resids[0]}")
+        # fake cluster dict with only one entry
+        cl_dict = {1: unique_sorted_resids}
+
+    # log data
+    for el in cl_dict.keys():
+        log.info(
+            f"cluster {el}, residues"
+            f" {' '.join([str(res) for res in cl_dict[el]])}"
+        )
+
+    # check if data must be flushed to output file
+    if output:
+        # initiate output directory
+        output_basepath = create_output_folder(output, uniprot_id='resclust')
+        # write txt file
+        output_fname = f'{output_basepath}/clustered_residues.out'
+        log.info(f'writing clusters data in "{output_fname}"')
+        with open(output_fname, 'w') as filout:
+            for el in cl_dict.keys():
+                filout.write(
+                    f"cluster {el} -> "
+                    f"{' '.join([str(res) for res in cl_dict[el]])}"
+                    "\n"
+                )
 
 
 if __name__ == "__main__":

tests/test_cli_resclust.py

@@ -2,6 +2,9 @@
 
 import pytest
 
+import os
+import shutil
+
 from arctic3d.cli_resclust import main
 
 from . import golden_data
@@ -22,6 +25,7 @@ def test_resclust_cli(example_pdbpath):
         7.0,
         "average",
         "distance",
+        None,
     )
 
 
@@ -35,6 +39,7 @@ def test_wrong_residue_list(example_pdbpath):
             9.0,
             "average",
             "distance",
+            None,
         )
     assert e.type == SystemExit
     assert e.value.code == 1
@@ -49,4 +54,20 @@ def test_resclust_maxclust(example_pdbpath):
         2,
         "average",
         "maxclust",
+        None,
+    )
+
+
+def test_resclust_genoutput(example_pdbpath):
+    main(
+        example_pdbpath,
+        "100,101,102,133,134,135",
+        None,
+        2,
+        "average",
+        "maxclust",
+        "resclustout",
     )
+    assert os.path.exists("resclustout") is True
+    assert os.path.exists("resclustout/clustered_residues.out") is True
+    shutil.rmtree("resclustout")