Sequence

Read

PyPropel reads a protein sequence in FASTA format with the pp.seq.read module.

Python

import pypropel as pp

seq = pp.seq.read(
    fasta_fpn=to('data/fasta/1aigL.fasta'),
)
print(seq)

Output

ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWNPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFAFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFFFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSAVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING

Save

A protein sequence can be saved.

Python

import pypropel as pp

seq = pp.seq.save(
    list_2d=[
        ['1aigL-new', seq],
    ],
    sv_fp=to('data/fasta/'),
)

Output

No.1 saving 1aigL-new in FASTA format.

Check empty

You can check if all sequences are empty.

Python

import pypropel as pp

prot_df = pd.DataFrame({
    'prot': ['1aig', '1aij', '1xqf'],
    'chain': ['L', 'L', 'A'],
})

seq = pp.seq.is_empty(
    prot_df=prot_df,
    fasta_fp=to('data/fasta/'),
    sv_empty_fp=to('data/'),
)

Output

27/07/2024 22:14:29 logger: ============>No0. protein 1aig chain L
27/07/2024 22:14:29 logger: ============>No1. protein 1aij chain L
27/07/2024 22:14:29 logger: ============>No2. protein 1xqf chain A
Finished

Check match

You can check if all sequences in one format match those in another format. Below shows if sequences in FASTA format match those in XML format.

Python

import pypropel as pp

prot_df = pd.DataFrame({
    'prot': ['1aig', '1aij', '1xqf'],
    'chain': ['L', 'L', 'A'],
})

seq = pp.seq.is_match(
    prot_df=prot_df,
    fasta_path=to('data/fasta/'),
    # pdb_path=to('data/pdb/pdbtm/'),
    xml_path=to('data/xml/'),
    kind='fasta<->xml',
    sv_mismatch_fp=to('data/'),
)

Output

27/07/2024 22:17:32 logger: ============>No0. protein 1aig chain L
27/07/2024 22:17:32 logger: ============>They match.
27/07/2024 22:17:32 logger: ============>No1. protein 1aij chain L
27/07/2024 22:17:32 logger: ============>They match.
27/07/2024 22:17:32 logger: ============>No2. protein 1xqf chain A
27/07/2024 22:17:32 logger: ============>They do not match.
Finished