seqres2atmseq

Align the SEQRES sequence with the ATMSEQ sequence of a protein chain and output a mask array (0: a missing residue in the ATMSEQ; 1: match)

Table of Contents

• seqres2atmseq
  • Table of Contents
  • Installation
  • Usage
    • Example: use fasta file as input
      • FASTA file format
    • Example: use SEQRES and ATMSEQ as input

---

Installation

If you are using a conda environment, you can install seqres2atmseq by:

$ pip install git+https://github.com/biochunan/seqres2atmseq.git

This will install a command-line tool seqres2atmseq in your conda environment.

Usage

Check help message:

$ seqres2atmseq -h  # see below 

Help message:

usage: seqres2atmseq [-h] [-i FASTA] [-s SEQRES] [-a ATMSEQ] [-n SEQ_NAME] [-c CLUSTAL_OMEGA_EXECUTABLE] [-o OUTPUT] [-v]

Process sequence file.

options:
  -h, --help            show this help message and exit
  -i FASTA, --fasta FASTA
                        Input FASTA file path
  -s SEQRES, --seqres SEQRES
                        SEQRES sequence
  -a ATMSEQ, --atmseq ATMSEQ
                        ATMSEQ sequence
  -n SEQ_NAME, --seq_name SEQ_NAME
                        Sequence name
  -c CLUSTAL_OMEGA_EXECUTABLE, --clustal_omega_executable CLUSTAL_OMEGA_EXECUTABLE
                        Path to clustal omega executable
  -o OUTPUT, --output OUTPUT
                        Output directory or file path
  -v, --verbose         Verbose mode

Example: use fasta file as input

Run alignment and save the mask json file with a FASTA file as input. We provie a test FASTA file seq.fasta in the test directory. Refer to FASTA file format for the FASTA file format.

# current directory: seqres2atmseq
$ seqres2atmseq -i test/test.fasta -o test/mask.json --verbose 

• -i: input FASTA file path
• -o: output file path
  • if the output file path is a directory, the output file will be saved in the directory with name mask.json
  • if the output file path is a file, the output file will be saved as the file
• --verbose: verbose mode, this will print the alignment result in the terminal

stdout:

2023-12-02 21:55:25.118 | DEBUG    | seqres2atmseq.app:main:275 - 
chocolate_A seqres: ADLQFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQSAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSDLHVDVKGYKDGGIHLECRSTGWYPQPQIQWSNNKGENIPTVEAPVVADGVGLYAVAASVIMRGSSGEGVSCTIRSSLLGLEKTASISIADPFFRSAQ
chocolate_A atmseq: ---QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQSAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSDLHVDVKGYKDGGIHLECRSTGWYPQPQIQWSNNKGENIPTVEAPVVADGVGLYAVAASVIM------GVSCTIRSSLLGLEKTASISIADPFF----
chocolate_A mask  : 0001111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111000000111111111111111111111111110000

2023-12-02 21:55:25.131 | DEBUG    | seqres2atmseq.app:main:275 - 
sunflower_B seqres: ADLQFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQSAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSDLHVDVKGYKDGGIHLECRSTGWYPQPQIQWSNNKGENIPTVEAPVVADGVGLYAVAASVIMRGSSGEGVSCTIRSSLLGLEKTASISIADPFFRSAQ
sunflower_B atmseq: ---QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQSAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSDLHVDVKGYKDGGIHLECRSTGWYPQPQIQWSNNKGENIPTVEAPVVADGVGLYAVAASVIM------GVSCTIRSSLLGLEKTASISIADPFF----
sunflower_B mask  : 0001111111111111111111111111111111111111111111111111111111111111111111111111111

FASTA file format

The FASTA file should be in the following format:

>chocolate_A|seqres
ADLQFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSS
>chocolate_A|atmseq
QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSS
>sunflower_B|atmseq
ADLQFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSS
>sunflower_B|seqres
ADLQFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSS

Each protein chain should have a pair of SEQRES and ATMSEQ sequences, as indicated by the suffix |seqres and |atmseq in the sequence header above. Each protein chain is distinguished by the prefix of the sequence header, e.g. chocolate_A and sunflower_B in the example above. This can be any string, but should be unique for each protein chain. For example, you can use PDB ID and chain id [pdbID]_[chainID] e.g. ABCD_A as the prefix.

Refer to the example FASTA file test/test.fasta in the test directory.

Example: use SEQRES and ATMSEQ as input

Run alignment and save the mask json file with SEQRES and ATMSEQ as input.

# current directory: seqres2atmseq
$ seqres2atmseq \
  -s \
  ADLQFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQSAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSDLHVDVKGYKDGGIHLECRSTGWYPQPQIQWSNNKGENIPTVEAPVVADGVGLYAVAASVIMRGSSGEGVSCTIRSSLLGLEKTASISIADPFFRSAQ \
  -a \ 
  QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQSAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSDLHVDVKGYKDGGIHLECRSTGWYPQPQIQWSNNKGENIPTVEAPVVADGVGLYAVAASVIMGVSCTIRSSLLGLEKTASISIADPFF \
  -n custom_identifier \ 
  -o test/mask.json \
  --verbose

• -s: SEQRES sequence
• -a: ATMSEQ sequence
• -n: sequence name, this will be used as the prefix of the sequence header in the output FASTA file, can be any string
  • if not provided, the sequence name will be seq
  • if there is space in the sequence name, wrap the name with quotes, e.g. -n 'my seq'
• -o: output file path
  • if the output file path is a directory, the output file will be saved in the directory with name mask.json
  • if the output file path is a file, the output file will be saved as the file
• --verbose: verbose mode, this will print the alignment result in the terminal

stdout:

2023-12-02 22:35:53.879 | DEBUG    | seqres2atmseq.app:main:275 - 
custom_identifier seqres: ADLQFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQSAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSDLHVDVKGYKDGGIHLECRSTGWYPQPQIQWSNNKGENIPTVEAPVVADGVGLYAVAASVIMRGSSGEGVSCTIRSSLLGLEKTASISIADPFFRSAQ
custom_identifier atmseq: ---QFSVLGPSGPILAMVGEDADLPCHLFPTMSAETMELKWVSSSLRQVVNVYADGKEVEDRQSAPYRGRTSILRDGITAGKAALRIHNVTASDSGKYLCYFQDGDFYEKALVELKVAALGSDLHVDVKGYKDGGIHLECRSTGWYPQPQIQWSNNKGENIPTVEAPVVADGVGLYAVAASVIM------GVSCTIRSSLLGLEKTASISIADPFF----
custom_identifier mask  : 0001111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111000000111111111111111111111111110000