Merge pull request #31 from aertslab/add_seqlet_coordinates_to_all_pa…

…tterns_dict add seqlet coordinates to all patterns dict
aertslab · Oct 2, 2024 · 07e4a25 · 07e4a25
2 parents a08d805 + f8fb728
commit 07e4a25
Show file tree

Hide file tree

Showing 2 changed files with 12 additions and 4 deletions.
diff --git a/src/crested/tl/_modisco_utils.py b/src/crested/tl/_modisco_utils.py
@@ -99,7 +99,6 @@ def _trim_pattern_by_ic(
 
     return _trim(pattern, start_idx, end_idx)
 
-
 def _trim(pattern: dict, start_idx: int, end_idx: int) -> dict:
     """
     Trims the pattern to the specified start and end indices.
@@ -117,10 +116,15 @@ def _trim(pattern: dict, start_idx: int, end_idx: int) -> dict:
     -------
         Trimmed pattern.
     """
+    # TODO: Reading the pattern from disk should really be done in a seperate function!
 
+    seqlet_dict = {}
+    # read seqlet information
+    for k in pattern["seqlets"].keys():
+        seqlet_dict[k] = pattern["seqlets"][k][:]
+    # do actual trimming
     seqlets_sequences = pattern['seqlets']['sequence']
     trimmed_sequences = [seq[start_idx:end_idx] for seq in seqlets_sequences]
-    seqlet_dict = {}
     seqlet_dict['sequence'] = trimmed_sequences
     return {
         "sequence": np.array(pattern["sequence"])[start_idx:end_idx],

diff --git a/src/crested/tl/_tfmodisco.py b/src/crested/tl/_tfmodisco.py
@@ -636,12 +636,16 @@ def process_patterns(
                                 f"{cell_type.replace(' ', '_')}_{metacluster_name}_{pattern_idx}"
                             )
                             is_pos = metacluster_name == "pos_patterns"
-                            trimmed_patterns.append(
-                                _trim_pattern_by_ic(
+                            pattern = _trim_pattern_by_ic(
                                     hdf5_results[metacluster_name][p],
                                     is_pos,
                                     trim_ic_threshold
                                 )
+                            # store file path so it is possible to track back
+                            # where the pattern comes from.
+                            pattern["file_path"] = h5_file
+                            trimmed_patterns.append(
+                                pattern
                             )
                             is_pattern_pos.append(is_pos)
                             pattern_idx = pattern_idx + 1