Overview

cdskit is a pre- and post-processing tool for protein-coding sequences. All sequence formats supported by biopython are available in this tool for both input and output.

Dependency

• python 3
• biopython
• numpy

Installation

# Installation with pip
pip install git+https://github.com/kfuku52/cdskit

# This should show complete options
cdskit -h 

Example

Padding truncated coding sequences to make them in-frame

cdskit pad --seqfile input.fasta --outfile output.fasta

# input.fasta
>miss_1nt_5prime
TGCTAAGCGGTAATCTAAGCGGTAATTGA
>miss_2nt_5prime
GCTAAGCGGTAATCTAAGCGGTAATTGA
>miss_1nt_3prime
ATGCTAAGCGGTAATCTAAGCGGTAATTG
>miss_2nt_3prime
ATGCTAAGCGGTAATCTAAGCGGTAATT
>miss_1nt_both
TGCTAAGCGGTAATCTAAGCGGTAATTG
>miss_2nt_both
GCTAAGCGGTAATCTAAGCGGTAATT
>complete
ATGCTAAGCGGTAATCTAAGCGGTAATTGA

# output.fasta
>miss_1nt_5prime
NTGCTAAGCGGTAATCTAAGCGGTAATTGA
>miss_2nt_5prime
NNGCTAAGCGGTAATCTAAGCGGTAATTGA
>miss_1nt_3prime
ATGCTAAGCGGTAATCTAAGCGGTAATTGN
>miss_2nt_3prime
ATGCTAAGCGGTAATCTAAGCGGTAATTNN
>miss_1nt_both
NTGCTAAGCGGTAATCTAAGCGGTAATTGN
>miss_2nt_both
NNGCTAAGCGGTAATCTAAGCGGTAATTNN
>complete
ATGCTAAGCGGTAATCTAAGCGGTAATTGA

Extracting longest sequences among isoforms using regular expression

cdskit aggregate --seqfile input.fasta --outfile output.fasta --expression ":.*" "\|.*"

# input.fasta
>seq1:1.length=30nt
ATGCTAAGCGGTAATCTAAGCGGTAATTGA
>seq1:2.length=327nt
ATGCTAAGCGGTAATCTAAGCGGTTGA
>seq1:3.length=33nt
ATGCAACTAAGCGGTAATCTAAGCGGTAATTGA
>seq2|1.length=45nt
ATGTCGGAATTGCGAGTAAGCACCAGCTTCTCAAAACCAAAATAA
>seq2|2.length=54nt
ATGTCGAGATCCCGAGAATTGCGAGTAAGCACCAGCTTCTCAAAACCAAAATAA

# output.fasta
>seq1:3.length=33nt
ATGCAACTAAGCGGTAATCTAAGCGGTAATTGA
>seq2|2.length=54nt
ATGTCGAGATCCCGAGAATTGCGAGTAAGCACCAGCTTCTCAAAACCAAAATAA

Mask ambiguous and/or stop codons

cdskit mask --seqfile input.fasta --outfile output.fasta

# input.fasta
>stop
---ATGTAAATTATGTTGAAG---
>ambiguous1
---ATGTNAATTATGTTGAAG---
>ambiguous2
---ATGT-AATTATGTTGAAG---
>all
---ATGTAAATT--GTTGANG---

# output.fasta
>stop
---ATGNNNATTATGTTGAAG---
>ambiguous1
---ATGNNNATTATGTTGAAG---
>ambiguous2
---ATGNNNATTATGTTGAAG---
>all
---ATGNNNATTNNNTTGNNN---

Pipe for streamlined analysis

cat input.fasta \
| cdskit pad \
| cdskit mask \
| cdskit aggregate \
> output.fasta

Licensing

This program is BSD-licensed (3 clause). See LICENSE for details.