Rename "comment" to "N_observed"

Author: Donaim

alldata/bblab_site/tools/isoforms_plot/index.html

@@ -474,7 +474,7 @@ <h3>Transcripts</h3>
 		</p>
 
 		<p>
-			Three optional fields control how transcripts appear: <code>label</code>, <code>group</code>, and <code>comment</code>. The <code>label</code> appears at the right side above the transcript (typically a gene or isoform name). The <code>group</code> field clusters related transcripts visually—transcripts sharing the same group name are drawn as a block, marked by a vertical line on the left edge of the plot. The <code>comment</code> appears on the right side of the transcript (commonly used for read counts or sample metadata).
+			Three optional fields control how transcripts appear: <code>label</code>, <code>group</code>, and <code>N_observed</code>. The <code>label</code> appears at the right side above the transcript (typically a gene or isoform name). The <code>group</code> field clusters related transcripts visually—transcripts sharing the same group name are drawn as a block, marked by a vertical line on the left edge of the plot. The <code>N_observed</code> appears on the right side of the transcript (commonly used for read counts or sample metadata).
 		</p>
 
 		<p>

alldata/bblab_site/tools/isoforms_plot/isoforms_plot/compiler.py

@@ -132,11 +132,14 @@ def compile_transcripts(
                     next_fragment=(next_part.start, next_part.end),
                 )
 
+        # Wrap N_observed in parentheses for display as comment
+        comment = f"({transcript.N_observed})" if transcript.N_observed else None
+
         compiled_transcripts.append(
             CompiledTranscript(
                 parts=parts_tuple,
                 label=transcript.label,
-                comment=transcript.comment,
+                comment=comment,
             )
         )
 
@@ -147,7 +150,7 @@ def compile_transcripts(
     for transcript in compiled_transcripts:
         current_label = transcript.label
         if current_label is not None and current_label == prev_label:
-            # Remove duplicate consecutive label
+            # Remove duplicate consecutive label (keep comment intact)
             deduplicated_transcripts.append(
                 CompiledTranscript(
                     parts=transcript.parts,

alldata/bblab_site/tools/isoforms_plot/isoforms_plot/parser.py

@@ -59,7 +59,7 @@ class Transcript:
     fragments: Sequence[Fragment]
     label: Optional[str]
     group: Optional[str]
-    comment: Optional[str]
+    N_observed: Optional[str]
 
 
 @dataclass(frozen=True)
@@ -91,7 +91,7 @@ def read_transcripts(reader: csv.DictReader) -> Iterator[Transcript]:
     Expected CSV columns:
     - fragments: Semicolon-separated list of ranges (e.g., "1-743; 4913-end")
     - label: Optional label for the transcript
-    - comment: Optional comment
+    - N_observed: Optional number of observations
     - group: Optional group name
 
     Each fragment is "start-end" where:
@@ -185,14 +185,14 @@ def read_transcripts(reader: csv.DictReader) -> Iterator[Transcript]:
 
         # Extract optional fields, converting empty strings to None
         label = (row.get("label") or "").strip() or None
-        comment = (row.get("comment") or "").strip() or None
+        N_observed = (row.get("N_observed") or "").strip() or None
         group = (row.get("group") or "").strip() or None
 
         yield Transcript(
             fragments=tuple(fragments),
             label=label,
             group=group,
-            comment=comment,
+            N_observed=N_observed,
         )
 
 

alldata/bblab_site/tools/isoforms_plot/test_isoforms.csv

@@ -3,30 +3,30 @@
 My Isoforms Plot Title
 
 [transcripts]
-fragments,label,comment,group
-1-743; 4913-end,vif,(3),My First Group
-1-743; 5390-end,vpr,(15),My First Group
-1-743; 4913-4962; 5390-end,vpr,(4),My First Group
-1-743; 5390-5463; 5976-end,vpu/env,(4),My First Group
-1-743; 5976-end,vpu/env,(1),My First Group
-1-743; 4913-4962; 5390-5463; 5976-end,vpu/env,(1),My First Group
-1-743; 5390-5463; 5976-6046; 8369-end,nef,(14),My First Group
-1-743; 4913-4962; 5390-5463; 5976-6046; 8369-end,nef,(7)
-1-743; 5976-6046; 8369-end,nef,(6)
-1-710; 5976-6046; 8369-end,nef,(2)
-1-743; 4913-4962; 5976-6046; 8369-end,nef,(2)
-1-743; 5390-5463; 5976-6046; 8369-end,nef,(1)
-1-743; 5777-6046; 8369-end,tat,(2)
-1-743; 5390-5463; 5777-6046; 8369-end,tat,(1)
-1-743; 4913-4962; 5390-5463; 5777-6046; 8369-end,tat,(1)
-1-743; 5390-5463; 5960-6046; 8369-end,rev,(3),My last group
-1-743; 5960-6046; 8369-end,rev,(3),My last group
-1-743; 5390-5463; 5954-6046; 8369-end,rev,(2),My last group
-1-743;  5954-6046; 8369-end,rev,(1),My last group
-1-743; 4913-4962; 5390-5463; 5960-6046; 8369-end,rev,(1),My last group
-1-743; 4913-4962; 5390-5463; 5954-6046; 8369-end,rev,(1),My last group
-1-743; 4913-4962; 5390-5463; 5954-end,example user input category,(1),My last group
-1-743; 4913-4962; 5390-5463; 6611-end,should not happen,(1),My last group
+fragments,label,N_observed,group
+1-743; 4913-end,vif,3,My First Group
+1-743; 5390-end,vpr,15,My First Group
+1-743; 4913-4962; 5390-end,vpr,4,My First Group
+1-743; 5390-5463; 5976-end,vpu/env,4,My First Group
+1-743; 5976-end,vpu/env,1,My First Group
+1-743; 4913-4962; 5390-5463; 5976-end,vpu/env,1,My First Group
+1-743; 5390-5463; 5976-6046; 8369-end,nef,14,My First Group
+1-743; 4913-4962; 5390-5463; 5976-6046; 8369-end,nef,7
+1-743; 5976-6046; 8369-end,nef,6
+1-710; 5976-6046; 8369-end,nef,2
+1-743; 4913-4962; 5976-6046; 8369-end,nef,2
+1-743; 5390-5463; 5976-6046; 8369-end,nef,1
+1-743; 5777-6046; 8369-end,tat,2
+1-743; 5390-5463; 5777-6046; 8369-end,tat,1
+1-743; 4913-4962; 5390-5463; 5777-6046; 8369-end,tat,1
+1-743; 5390-5463; 5960-6046; 8369-end,rev,3,My last group
+1-743; 5960-6046; 8369-end,rev,3,My last group
+1-743; 5390-5463; 5954-6046; 8369-end,rev,2,My last group
+1-743;  5954-6046; 8369-end,rev,1,My last group
+1-743; 4913-4962; 5390-5463; 5960-6046; 8369-end,rev,1,My last group
+1-743; 4913-4962; 5390-5463; 5954-6046; 8369-end,rev,1,My last group
+1-743; 4913-4962; 5390-5463; 5954-end,example user input category,1,My last group
+1-743; 4913-4962; 5390-5463; 6611-end,should not happen,1,My last group
 
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