From b8eef73a4805d2e6feb579eb932f000723abe330 Mon Sep 17 00:00:00 2001
From: Larissa Glass <larissa.glass@unibas.ch>
Date: Wed, 9 Nov 2022 13:46:50 +0100
Subject: [PATCH] Display progress bar for main processing loop
---
environment.yml | 1 +
pyproject.toml | 1 +
tsg/main.py | 4 +++-
3 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/environment.yml b/environment.yml
index 3287b74..ac26257 100644
--- a/environment.yml
+++ b/environment.yml
@@ -7,6 +7,7 @@ dependencies:
- matplotlib
- pandas
- pip
+ - tqdm
- flake8-docstrings
- mypy
- flake8
diff --git a/pyproject.toml b/pyproject.toml
index ed805ec..de522e9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,6 +12,7 @@ requires-python = ">=3.7"
license = {text = "MIT"}
dependencies = [
"pandas",
+ "tqdm",
]
[project.urls]
diff --git a/tsg/main.py b/tsg/main.py
index 25b7455..29e1420 100644
--- a/tsg/main.py
+++ b/tsg/main.py
@@ -2,6 +2,8 @@ import logging
import numpy as np
import pandas as pd
+from tqdm import tqdm
+
LOG = logging.getLogger(__name__)
@@ -288,7 +290,7 @@ def sample_transcripts(
# Set up output file, write header once and append data in loop
write_header(output_annotations_file)
- for _, row in transcripts.iterrows():
+ for _, row in tqdm(transcripts.iterrows()):
transcript_id = row["id"]
transcript_count = row["count"]
--
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