From 92fb2a0500b2a29b78887bdc6a3e285b16caee96 Mon Sep 17 00:00:00 2001
From: ivan-aksamentov <ivan.aksamentov@gmail.com>
Date: Thu, 2 Jan 2025 21:49:20 +0100
Subject: [PATCH] feat: use json string to store additional metadata in fasta
 headers

Proposal is to use stringified JSON to add any additional data to fasta headers as opposed to home-grown format.

Advantages:
 - Easire to parse: the fasta header can be split on first space and then the second part can be parsed as json to extract all metadata, which is basically 2 lines of code in most languages. The home-grown format would either have to be parsed specifically or cannot be parsed reliably at all, especially if not documented.
- Output contains field names, which might improve clarity if the meaning of values is not immediately obvious
 - New fields can be easily added and removed without any additional thinking about new delimiters, positions etc.
 - We could even define a schema and document the format to be super-strict and clear! (but probably too much for this particular case)
- JSON is a compromise between human- and machine-readability

Disadvantages:
- Need to double check if fasta headers allows json characters
- Output is longer than just ad-hoc values
- Output contains field names, which might be excessive if the meaning is already clear
- JSON is a compromise between human- and machine-readability

Example outputs:

Before:
```
>11571779012938514380 pCAV1344-40-1705098846223677255 [4961-9839|+]
```

After:
```
>11571779012938514380 {"path_name":"pCAV1344-40","block_id":1705098846223677255,"start":4961,"end":9839,"strand":"+"}
```
---
 .../pangraph/src/pangraph/pangraph_block.rs     | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/packages/pangraph/src/pangraph/pangraph_block.rs b/packages/pangraph/src/pangraph/pangraph_block.rs
index 1e24ec70..a1442c6f 100644
--- a/packages/pangraph/src/pangraph/pangraph_block.rs
+++ b/packages/pangraph/src/pangraph/pangraph_block.rs
@@ -1,3 +1,4 @@
+use crate::io::json::{json_write_str, JsonPretty};
 use crate::io::seq::reverse_complement;
 use crate::pangraph::edits::Edit;
 use crate::pangraph::pangraph::Pangraph;
@@ -10,6 +11,7 @@ use getset::{CopyGetters, Getters};
 use maplit::btreemap;
 use schemars::JsonSchema;
 use serde::{Deserialize, Serialize};
+use serde_json::json;
 use std::collections::{BTreeMap, BTreeSet};
 use std::hash::Hash;
 
@@ -154,7 +156,20 @@ impl PangraphBlock {
           let path_name = &graph.paths[&node.path_id()].name().as_ref().unwrap();
           let (start, end) = node.position();
           let strand = node.strand();
-          format!("{node_id} {path_name}-{block_id} [{start}-{end}|{strand}]")
+
+          let meta = json_write_str(
+            &json! ({
+              "path_name": path_name,
+              "block_id": block_id,
+              "start": start,
+              "end": end,
+              "strand": strand,
+            }),
+            JsonPretty(false),
+          )
+          .unwrap();
+
+          format!("{node_id} {meta}")
         }
         RecordNaming::Path => {
           let path_id = graph.nodes[node_id].path_id();