Reformat

Reformat#

It is necessary to convert between MSAs in different formats. In HHblits, the Reformat method can support this function.

In this tutorial, we will show how we can convert between MSAs from the Stockholm format to the A3M format.

Example usage#

First, let’s prepare identifiers of some transmembrane proteins and make them recognisable in Python, like this.

prots = [
    ['6e3y', 'E'],
    ['6rfq', 'S'],
    ['6t0b', 'm'],
]
import pandas as pd
df = pd.DataFrame(prots, columns=['prot', 'chain'])

We need to specify all parameters used for generating the HHblits commands. They mainly include reformat_fp, input_fp, and sv_fp.

Please make sure that you have installed HHblits software. If not, please refer to this tutorial for how to install HHblits. In our case, an executable of the HHblits program is in ./hhblits/scripts/.

Please specify the path sv_fp that you want to save the reformatted MSAs in the a3m format.

reformat_fp = './hhblits/scripts/'
input_fp ='./data/a3m/'
sv_fp ='./data/a3m/reformat/'

Let’s then generate the MSAs for these proteins defined above by using the following codes. Of course, there are many more parameters other than the four above and you can change the values of Attributes below.

import tmkit as tmk

for id in df.index:
    prot_name = df.loc[id, 'prot']
    seq_chain = df.loc[id, 'chain']
    tmk.msa.run_format(
        reformat_fp=reformat_fp,
        max_length_per_name_line=1500,
        aa_per_line=1500,
        input_format='sto',
        output_format='a3m',
        input_fpn=input_fp + prot_name + seq_chain + '.sto',
        output_fpn=sv_fp + prot_name + seq_chain + '.a3m',

        # if you won't do it on clusters, please give False to the parameter send2cloud
        send2cloud=False,
        cloud_cmd="",

        # send2cloud=True,
        # cloud_cmd="qsub -q all.q -N 'jsun'",
    )

Attributes#

Attribute

Description

reformat_fp

path where an executable of Reformat is placed

input_fp

path where a protein sequence database is placed

sv_fp

path to where you want to save the MSAs in the a3m format

input_format

input format, e.g., .sto for the Stockholm format

output_format

output format, e.g., .a3m for the a3m format

max_length_per_name_line

maximum number of characers in nameline (default=1000)

aa_per_line

number of residues per line (for Clustal, FASTA, A2M, A3M formats) (default=100)

See also

We encourage users to check the meaning of all parameters via this route. Please see here for better understanding the file-naming system.

Output#

Finally, you will see the following output showing the generated commands. It will tell Reformat how to search MSAs.

===>The current order: ./hhblits/scripts/reformat.pl -d 1500 -l 1500 sto a3m ./data/a3m/6e3yE.sto ./data/a3m/reformat/6e3yE.a3m
===>The current order: ./hhblits/scripts/reformat.pl -d 1500 -l 1500 sto a3m ./data/a3m/6rfqS.sto ./data/a3m/reformat/6rfqS.a3m
===>The current order: ./hhblits/scripts/reformat.pl -d 1500 -l 1500 sto a3m ./data/a3m/6t0bm.sto ./data/a3m/reformat/6t0bm.a3m
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