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base repository: haessar/peaks2utr
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base: v1.4.0
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head repository: haessar/peaks2utr
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compare: master
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  • 8 commits
  • 6 files changed
  • 1 contributor

Commits on Nov 27, 2024

  1. Add files via upload

    haessar authored Nov 27, 2024

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  2. new logo in README

    haessar authored Nov 27, 2024

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Commits on Nov 28, 2024

  1. Add files via upload

    haessar authored Nov 28, 2024

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  2. Update README.md

    haessar authored Nov 28, 2024

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  3. Merge pull request #38 from haessar/haessar-patch-1

    Update README.md
    haessar authored Nov 28, 2024

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Commits on Feb 6, 2025

  1. simple fix for issue Keyerror 'ID' on --gtf option #41

    haessar committed Feb 6, 2025
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  2. fix for actions/upload-artifact@v3 deprecated bug

    haessar committed Feb 6, 2025
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Commits on Feb 10, 2025

  1. Merge pull request #42 from haessar/hot-fix

    haessar authored Feb 10, 2025

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Showing with 78 additions and 4 deletions.
  1. +1 −1 .github/workflows/ci.yml
  2. +1 −1 README.md
  3. +1 −1 peaks2utr/collections.py
  4. BIN peaks2utr_2024.png
  5. +74 −0 peaks2utr_2024.svg
  6. +1 −1 setup.cfg
2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
Original file line number Diff line number Diff line change
@@ -26,7 +26,7 @@ jobs:
with:
python-version: ${{ matrix.python-version }}
- name: Cache APT Packages (Linux)
uses: awalsh128/cache-apt-pkgs-action@v1.3.0
uses: awalsh128/cache-apt-pkgs-action@v1.4.3
with:
packages: bedtools genometools
version: 1.0
2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
@@ -5,7 +5,7 @@
[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
[![DOI](https://zenodo.org/badge/428231055.svg)](https://zenodo.org/badge/latestdoi/428231055)

<img width="400" src="https://user-images.githubusercontent.com/11962461/172829916-c2fa81e6-7ae5-4c9a-a758-c3ba4c4198cb.png">
<img width="400" src="peaks2utr_2024.png">

peaks2utr is a Python command-line tool that annotates 3' untranslated regions (UTR) for a given set of aligned sequencing reads in BAM format, and canonical annotation in GFF or GTF format. peaks2utr uses MACS (https://pypi.org/project/MACS2/) to call broad "peaks" of significant read coverage in the BAM file, and uses those peaks that pass a set of criteria as a basis to annotate novel 3' UTRs. This favours BAM files from the likes of 10x Chromium runs, where signal is inherently concentrated at the distal ends of the 3' or 5' UTRs. Reads containing soft-clipped bases and polyA-tails of a given length are detected, and their end bases tallied as "truncation points". When piled up, each co-occurring truncation point is used to determine the precise end base of a given UTR. peaks2utr can be tuned to extend, override or ignore any pre-existing 3' UTR annotations in the input GFF file.

2 changes: 1 addition & 1 deletion peaks2utr/collections.py
Original file line number Diff line number Diff line change
@@ -73,7 +73,7 @@ def _apply_gtf_dialect(feature, attrs, gene_id=None):
else:
attrs['gene_id'] = gene_id
attrs['transcript_id'] = attrs.pop('Parent')
attrs.pop('ID')
attrs.pop('ID', None)
else:
attrs['gene_id'] = attrs.pop('ID')

Binary file added peaks2utr_2024.png
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74 changes: 74 additions & 0 deletions peaks2utr_2024.svg
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2 changes: 1 addition & 1 deletion setup.cfg
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[metadata]
name = peaks2utr
version = 1.4.0
version = 1.4.1
author = William Haese-Hill
author_email = william.haese-hill@glasgow.ac.uk
description = A robust, parallelized Python CLI for annotating three_prime_UTR