https://github.com/nylander/fastear
FastEAR - Fast(er) Extraction of Alignment Regions from FASTA
https://github.com/nylander/fastear
faidx fasta samtools
Last synced: about 1 year ago
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FastEAR - Fast(er) Extraction of Alignment Regions from FASTA
- Host: GitHub
- URL: https://github.com/nylander/fastear
- Owner: nylander
- License: mit
- Created: 2020-04-25T22:32:42.000Z (about 6 years ago)
- Default Branch: main
- Last Pushed: 2024-09-11T12:54:09.000Z (over 1 year ago)
- Last Synced: 2024-09-11T19:54:46.951Z (over 1 year ago)
- Topics: faidx, fasta, samtools
- Language: Shell
- Homepage:
- Size: 34.2 KB
- Stars: 1
- Watchers: 2
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# FastEAR - Fast(er) Extraction of Alignment Regions
- Last modified: ons sep 11, 2024 02:53
- Sign: JN
## Description
Shell (bash) scripts for extracting regions from a fasta-formatted nucleotide
alignment based on the description of ranges in a [partitions
file](#example-partitions-file).
The scripts act as a wrapper for the main software that performs the
extraction: faidx. GNU parallel is used for doing the extraction in parallel.
The string in the first column of the partitions file will be used as the stem
of the output file name, and the suffix `.fas` will be added (for example:
`Apa.fas`). The output file will contain all fasta entries in the input fasta
file, but only with the sequence positions as specified in the partitions file.
Note that only the first string (without white-space characters!) in the fasta
headers will be used in the output.
Currently two versions of the script is provided, differing in which version of
faidx used (see [Requirements and
Installation](#requirements-and-installation)).
*Update*: A script using bedtools for extraction is also provided (see [Requirements and
Installation](#requirements-and-installation)).
## Usage
$ ./fastear_.sh fasta.fas partitions.txt
Example:
$ ./fastear_samtools-1.10.sh data/fasta.fas data/partitions.txt
## Example partitions file
Apa = 1-100
Bpa = 101-200
Cpa = 201-300
Dpa = 301-400
Epa = 401-484
## Requirements and Installation
Make sure to install [GNU parallel](https://www.gnu.org/software/parallel/),
and faidx. For faidx, I tried both the python version, pyfaidx
([https://pypi.org/project/pyfaidx](https://pypi.org/project/pyfaidx)), and the
original version from samtools
([https://github.com/samtools/samtools](https://github.com/samtools/samtools)).
Samtools v1.10 is available from, e.g., Ubuntu Linux repositories:
$ sudo apt install samtools
The syntax for samtools faidx have changed between minor samtools versions, and
there are two versions of the fastear-script supplied; one for samtools v1.7, and
one for v1.10 (or above. Last tested with v1.15).
In addition, if one wishes to use the "bedtools"-version, then `bedtools` needs
to be installed (tested using v2.27). For example (on ubuntu):
$ sudo apt install bedtools
Finally, put the fastear-script(s) in your PATH (e.g., `cp fastear_*.sh ~/bin/`).
## Timings
From a fasta file with 146 sequences, each with length 6,180,000 bp, we
extracted 4,818 alignments (on a GNU/Linux system with two Intel Xeon Silver
4214 CPU @ 2.20GHz, 48 cores in total):
#### Using GNU parallel
# fastear pyfaidx v.0.5.8 parallel
$ time fastear_pyfaidx.sh data.fas partitions.txt
real 0m47,499s
user 16m44,924s
sys 3m8,175s
# fastear samtools faidx v.1.7 parallel
$ time fastear_samtools-1.7.sh data.fas partitions.txt
real 0m19,714s
user 1m43,326s
sys 1m18,667s
# fastear samtools faidx v.1.10 parallel
$ time fastear_samtools-1.10.sh data.fas partitions.txt
real 0m20,172s
user 1m31,063s
sys 1m12,016s
# fastear bedtools parallel
$ time fastear_bedtools.sh data.fas partitions.txt
real 0m19,784s
user 1m3,445s
sys 0m53,333s
#### Using a "while read"-loop over the partitions file
# fastear pyfaidx v.0.5.8 serial
$ time fastear_pyfaidx.serial.sh data.fas partitions.txt
real 11m16,616s
user 9m50,814s
sys 2m11,124s
# fastear samtools faidx v.1.7 serial
$ time fastear_samtools-1.7.serial.sh data.fas partitions.txt
real 2m2,562s
user 1m33,131s
sys 0m53,938s
# fastear samtools faidx v.1.10 serial
$ time fastear_samtools-1.10.serial.sh data.fas partitions.txt
real 1m47,825s
user 1m18,883s
sys 0m52,152s
*Conclusions*: speed of extraction is faster using parallelization.
In addition, different implementations differ in speed. From
the examples above, faidx from bedtools or samtools (v.1.10) seems
preferable.
## Disclaimer
Currently in beta version, with minimal error checking. *Caveat emptor!*
## License and Copyright
Copyright (C) 2020-2024 Johan Nylander .
Distributed under terms of the [MIT license](LICENSE).