From 5ae1603d5a6caa79fe2d5295904a9bda7cdc4b8b Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Thu, 11 Jan 2024 16:19:07 +0100
Subject: [PATCH] script to remove replicon version
---
.../df-wiki-cli/df_wiki_cli/content/main.py | 42 +++++++++++++++++--
1 file changed, 39 insertions(+), 3 deletions(-)
diff --git a/packages/df-wiki-cli/df_wiki_cli/content/main.py b/packages/df-wiki-cli/df_wiki_cli/content/main.py
index 1affaa6b..e516f383 100644
--- a/packages/df-wiki-cli/df_wiki_cli/content/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/content/main.py
@@ -13,6 +13,7 @@ from pydantic import BaseModel, ValidationError
import frontmatter
from enum import Enum
from rich.console import Console
+import re
console = Console()
app = typer.Typer()
@@ -216,9 +217,9 @@ def systems(
if "article" in table_data:
sanitizedMetadata["doi"] = table_data["article"]["doi"]
if "abstract" in table_data["article"]:
- sanitizedMetadata["abstract"] = table_data["article"][
- "abstract"
- ]
+ sanitizedMetadata["abstract"] = table_data[
+ "article"
+ ]["abstract"]
del table_data["article"]
if "PFAM" in table_data:
del table_data["PFAM"]
@@ -241,3 +242,38 @@ def pae2png(tsv_file, png_file):
plt.tight_layout()
plt.savefig(png_file, dpi=150, facecolor=None, transparent=True)
plt.close()
+
+
+@app.command()
+def refseq(
+ input: Annotated[
+ Path,
+ typer.Option(
+ exists=False,
+ file_okay=True,
+ writable=True,
+ ),
+ ],
+ output: Annotated[
+ Path,
+ typer.Option(
+ file_okay=True,
+ dir_okay=False,
+ writable=True,
+ resolve_path=True,
+ ),
+ ],
+):
+
+ with open(output, "w") as out, open(input, "r") as refseq_f:
+ reader = csv.DictReader(refseq_f)
+ fieldnames = reader.fieldnames
+ writer = csv.DictWriter(out, fieldnames=fieldnames)
+ writer.writeheader()
+ for row in reader:
+ result = re.sub(r"^(\w+)\.\d+(_.*)$", r"\1\2", row["sys_id"])
+ console.print(f"[green]{row['sys_id']} -> {result}")
+ row["sys_id"] = result
+ writer.writerow(row)
+
+
\ No newline at end of file
--
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