Gapmm2: gapped alignment using minimap2 (align transcripts to genome)

Related tags

Deep Learninggapmm2
Overview

Latest Github release Conda

gapmm2: gapped alignment using minimap2

This tool is a wrapper for minimap2 to run spliced/gapped alignment, ie aligning transcripts to a genome. You are probably saying, yes minimap2 runs this with -x splice --cs option (you are correct). However, there are instances where the terminal exons from stock minimap2 alignments are missing. This tool detects those alignments that have unaligned terminal eons and uses edlib to find the terminal exon positions. The tool then updates the PAF output file with the updated information.

Rationale

We can pull out a gene model in GFF3 format that has a short 5' terminal exon:

scaffold_9	funannotate	gene	408904	409621	.	-	.	ID=OPO1_006919;
scaffold_9	funannotate	mRNA	408904	409621	.	-	.	ID=OPO1_006919-T1;Parent=OPO1_006919;product=hypothetical protein;
scaffold_9	funannotate	exon	409609	409621	.	-	.	ID=OPO1_006919-T1.exon1;Parent=OPO1_006919-T1;
scaffold_9	funannotate	exon	409320	409554	.	-	.	ID=OPO1_006919-T1.exon2;Parent=OPO1_006919-T1;
scaffold_9	funannotate	exon	409090	409255	.	-	.	ID=OPO1_006919-T1.exon3;Parent=OPO1_006919-T1;
scaffold_9	funannotate	exon	408904	409032	.	-	.	ID=OPO1_006919-T1.exon4;Parent=OPO1_006919-T1;
scaffold_9	funannotate	CDS	409609	409621	.	-	0	ID=OPO1_006919-T1.cds;Parent=OPO1_006919-T1;
scaffold_9	funannotate	CDS	409320	409554	.	-	2	ID=OPO1_006919-T1.cds;Parent=OPO1_006919-T1;
scaffold_9	funannotate	CDS	409090	409255	.	-	1	ID=OPO1_006919-T1.cds;Parent=OPO1_006919-T1;
scaffold_9	funannotate	CDS	408904	409032	.	-	0	ID=OPO1_006919-T1.cds;Parent=OPO1_006919-T1;

If we then map this transcript against the genome, we get the following PAF alignment.

$ minimap2 -x splice --cs genome.fasta cds-transcripts.fa | grep 'OPO1_006919'
OPO1_006919-T1	543	13	543	-	scaffold_9	658044	408903	409554	530	530	60	NM:i:0	ms:i:530	AS:i:466	nn:i:0	ts:A:+	tp:A:P	cm:i:167	s1:i:510	s2:i:0	de:f:0	rl:i:0	cs:Z::129~ct57ac:166~ct64ac:235

The --cs flag in minimap2 can be used to parse the coordinates (below) and you can see we are missing the 5' exon.

>>> cs2coords(408903, 13, 543, '-', ':129~ct57ac:166~ct64ac:235')
([(409320, 409554), (409090, 409255), (408904, 409032)],

So if we run this same alignment with gapmm2 we are able to properly align the 5' terminal exon.

$ gapmm2 genome.fa cds-transcripts.fa | grep 'OPO1_006919'
OPO1_006919-T1	543	0	543	-	scaffold_9	658044	408903	409621	543	543	60	tp:A:P	ts:A:+	NM:i:0	cs:Z::129~ct57ac:166~ct64ac:235~ct54ac:13

>>> cs2coords(408903, 0, 543, '-', ':129~ct57ac:166~ct64ac:235~ct54ac:13')
([(409609, 409621), (409320, 409554), (409090, 409255), (408904, 409032)]

Usage:

gapmm2 can be run as a command line script:

$ gapmm2
usage: gapmm2 [-o] [-t] [-m] [-d] [-h] [--version] reference query

gapmm2: gapped alignment with minimap2. Performs minimap2/mappy alignment with splice options and refines terminal alignments with edlib. Output is PAF format.

Positional arguments:
  reference         reference genome (FASTA)
  query             transcipts in FASTA or FASTQ

Optional arguments:
  -o , --out        output in PAF format (default: stdout)
  -t , --threads    number of threads to use with minimap2 (default: 3)
  -m , --min-mapq   minimum map quality value (default: 1)
  -d, --debug       write some debug info to stderr (default: False)

Help:
  -h, --help        Show this help message and exit
  --version         Show program's version number and exit

It can also be run as a python module. The splice_aligner function will return a list of lists containing PAF formatted data for each alignment and a dictionary of simple stats.

>>> from gapmm2.align import splice_aligner
>>> results, stats = splice_aligner('genome.fa', 'transcripts.fa')
>>> stats
{'n': 6926, 'low-mapq': 0, 'refine-left': 409, 'refine-right': 63}
>>> len(results)
6926
>>> results[0]
['OPO1_000001-T1', 2184, 0, 2184, '+', 'scaffold_1', 1803704, 887, 3127, 2184, 2184, 60, 'tp:A:P', 'ts:A:+', 'NM:i:0', 'cs:Z::958~gt56ag:1226']
>>>

To install the python package, you can do this with pip:

python -m pip install gapmm2

To install the most updated code in master you can run:

python -m pip install git+https://github.com/nextgenusfs/gapmm2.git
You might also like...
[NAACL & ACL 2021] SapBERT: Self-alignment pretraining for BERT.
[NAACL & ACL 2021] SapBERT: Self-alignment pretraining for BERT.

SapBERT: Self-alignment pretraining for BERT This repo holds code for the SapBERT model presented in our NAACL 2021 paper: Self-Alignment Pretraining

Cambridge Language Technology Lab 104 Dec 7, 2022
the code of the paper: Recurrent Multi-view Alignment Network for Unsupervised Surface Registration (CVPR 2021)
the code of the paper: Recurrent Multi-view Alignment Network for Unsupervised Surface Registration (CVPR 2021)

RMA-Net This repo is the implementation of the paper: Recurrent Multi-view Alignment Network for Unsupervised Surface Registration (CVPR 2021). Paper

Wanquan Feng 205 Nov 9, 2022
Pytorch implementation for
Pytorch implementation for "Implicit Feature Alignment: Learn to Convert Text Recognizer to Text Spotter".

Implicit Feature Alignment: Learn to Convert Text Recognizer to Text Spotter This is a pytorch-based implementation for paper Implicit Feature Alignme

wangtianwei 61 Nov 12, 2022
The PyTorch improved version of TPAMI 2017 paper: Face Alignment in Full Pose Range: A 3D Total Solution.
The PyTorch improved version of TPAMI 2017 paper: Face Alignment in Full Pose Range: A 3D Total Solution.

Face Alignment in Full Pose Range: A 3D Total Solution By Jianzhu Guo. [Updates] 2020.8.30: The pre-trained model and code of ECCV-20 are made public

Jianzhu Guo 3.4k Jan 2, 2023
🧠 A PyTorch implementation of 'Deep CORAL: Correlation Alignment for Deep Domain Adaptation.', ECCV 2016
🧠 A PyTorch implementation of 'Deep CORAL: Correlation Alignment for Deep Domain Adaptation.', ECCV 2016

Deep CORAL A PyTorch implementation of 'Deep CORAL: Correlation Alignment for Deep Domain Adaptation. B Sun, K Saenko, ECCV 2016' Deep CORAL can learn

Andy Hsu 200 Dec 25, 2022
An official implementation of the paper Exploring Sequence Feature Alignment for Domain Adaptive Detection Transformers
An official implementation of the paper Exploring Sequence Feature Alignment for Domain Adaptive Detection Transformers

Sequence Feature Alignment (SFA) By Wen Wang, Yang Cao, Jing Zhang, Fengxiang He, Zheng-jun Zha, Yonggang Wen, and Dacheng Tao This repository is an o

WangWen 79 Dec 24, 2022
Collective Multi-type Entity Alignment Between Knowledge Graphs (WWW'20)

CG-MuAlign A reference implementation for "Collective Multi-type Entity Alignment Between Knowledge Graphs", published in WWW 2020. If you find our pa

Bran Zhu 28 Dec 11, 2022
Seeing Dynamic Scene in the Dark: High-Quality Video Dataset with Mechatronic Alignment (ICCV2021)
Seeing Dynamic Scene in the Dark: High-Quality Video Dataset with Mechatronic Alignment (ICCV2021)

Seeing Dynamic Scene in the Dark: High-Quality Video Dataset with Mechatronic Alignment This is a pytorch project for the paper Seeing Dynamic Scene i

DV Lab 21 Nov 28, 2022
The tl;dr on a few notable transformer/language model papers + other papers (alignment, memorization, etc).
The tl;dr on a few notable transformer/language model papers + other papers (alignment, memorization, etc).

The tl;dr on a few notable transformer/language model papers + other papers (alignment, memorization, etc).

Will Thompson 166 Jan 4, 2023
Releases(v0.2.0)
Owner
Jon Palmer
Jon Palmer
GitHub Repository
Dilated Convolution for Semantic Image Segmentation

Multi-Scale Context Aggregation by Dilated Convolutions Introduction Properties of dilated convolution are discussed in our ICLR 2016 conference paper

Fisher Yu 764 Dec 26, 2022
Official code for: A Probabilistic Hard Attention Model For Sequentially Observed Scenes

"A Probabilistic Hard Attention Model For Sequentially Observed Scenes" Authors: Samrudhdhi Rangrej, James Clark Accepted to: BMVC'21 A recurrent atte

5 Nov 19, 2022
Implicit MLE: Backpropagating Through Discrete Exponential Family Distributions

torch-imle Concise and self-contained PyTorch library implementing the I-MLE gradient estimator proposed in our NeurIPS 2021 paper Implicit MLE: Backp

UCL Natural Language Processing 249 Jan 03, 2023
Loopy belief propagation for factor graphs on discrete variables, in JAX!

PGMax implements general factor graphs for discrete probabilistic graphical models (PGMs), and hardware-accelerated differentiable loopy belief propagation (LBP) in JAX.

Vicarious 62 Dec 23, 2022
Combining Reinforcement Learning and Constraint Programming for Combinatorial Optimization

Hybrid solving process for combinatorial optimization problems Combinatorial optimization has found applications in numerous fields, from aerospace to

117 Dec 13, 2022
Object Detection using YOLO from PyImageSearch

Object Detection using YOLO from PyImageSearch By applying object detection, you’ll not only be able to determine what is in an image, but also where

Mohamed NIANG 1 Feb 09, 2022
A library for uncertainty representation and training in neural networks.

Epistemic Neural Networks A library for uncertainty representation and training in neural networks. Introduction Many applications in deep learning re

DeepMind 211 Dec 12, 2022
Script for getting information in discord

User-info.py Script for getting information in https://discord.com/ Instalação: apt-get update -y apt-get upgrade -y apt-get install git pkg install

Moleey 1 Dec 18, 2021
Eff video representation - Efficient video representation through neural fields

Neural Residual Flow Fields for Efficient Video Representations 1. Download MPI

41 Jan 06, 2023
When in Doubt: Improving Classification Performance with Alternating Normalization

When in Doubt: Improving Classification Performance with Alternating Normalization Findings of EMNLP 2021 Menglin Jia, Austin Reiter, Ser-Nam Lim, Yoa

Menglin Jia 13 Nov 06, 2022
AntroPy: entropy and complexity of (EEG) time-series in Python

AntroPy is a Python 3 package providing several time-efficient algorithms for computing the complexity of time-series. It can be used for example to e

Raphael Vallat 153 Dec 27, 2022
[ICME 2021 Oral] CORE-Text: Improving Scene Text Detection with Contrastive Relational Reasoning

CORE-Text: Improving Scene Text Detection with Contrastive Relational Reasoning This repository is the official PyTorch implementation of CORE-Text, a

Jingyang Lin 18 Aug 11, 2022
Official Pytorch implementation of "Beyond Static Features for Temporally Consistent 3D Human Pose and Shape from a Video", CVPR 2021

TCMR: Beyond Static Features for Temporally Consistent 3D Human Pose and Shape from a Video Qualtitative result Paper teaser video Introduction This r

Hongsuk Choi 215 Jan 06, 2023
Predict and time series avocado hass

RECOMMENDER SYSTEM MARKETING TỔNG QUAN VỀ HỆ THỐNG DỮ LIỆU 1. Giới thiệu - Tiki là một hệ sinh thái thương mại "all in one", trong đó có tiki.vn, là

hieulmsc 3 Jan 10, 2022
An Approach to Explore Logistic Regression Models

User-centered Regression An Approach to Explore Logistic Regression Models This tool applies the potential of Attribute-RadViz in identifying correlat

0 Nov 12, 2021
Implementation of Analyzing and Improving the Image Quality of StyleGAN (StyleGAN 2) in PyTorch

Implementation of Analyzing and Improving the Image Quality of StyleGAN (StyleGAN 2) in PyTorch

Kim Seonghyeon 2.2k Jan 01, 2023
Creating a Linear Program Solver by Implementing the Simplex Method in Python with NumPy

Creating a Linear Program Solver by Implementing the Simplex Method in Python with NumPy Simplex Algorithm is a popular algorithm for linear programmi

Reda BELHAJ 2 Oct 12, 2022
A PyTorch Implementation of "Neural Arithmetic Logic Units"

Neural Arithmetic Logic Units [WIP] This is a PyTorch implementation of Neural Arithmetic Logic Units by Andrew Trask, Felix Hill, Scott Reed, Jack Ra

Kevin Zakka 181 Nov 18, 2022
PyTorch-lightning implementation of the ESFW module proposed in our paper Edge-Selective Feature Weaving for Point Cloud Matching

Edge-Selective Feature Weaving for Point Cloud Matching This repository contains a PyTorch-lightning implementation of the ESFW module proposed in our

5 Feb 14, 2022
Small repo describing how to use Hugging Face's Wav2Vec2 with PyCTCDecode

🤗 Transformers Wav2Vec2 + PyCTCDecode Introduction This repo shows how 🤗 Transformers can be used in combination with kensho-technologies's PyCTCDec

Patrick von Platen 102 Oct 22, 2022