Python packages

source: Python/README.md

This directory hosts some Python packages, though it is harder to separate them from other mainstream applications.

Special notes are given here regarding biopython, i.e.,

with data from UniProt, e.g., APOB and A1BG, whose setup is as follows,

wget https://rest.uniprot.org/uniprotkb/P04114.txt
wget https://rest.uniprot.org/uniprotkb/P04217.fasta
source ~/rds/public_databases/software/py38/bin/activate
 

Our Python script to handle them is listed below.

# all information
from Bio import SwissProt
with open('P04217.txt') as file:
    for record in SwissProt.parse(file):
        print(f"ID: {record.entry_name}, Description: {record.description}")
        for feature in record.features:
            print(feature)
        print("=" * 30)
        print("Sequence:")
        print(record.sequence)

# match and position
def match_sequence(fasta_file, search_string):
    sequences = SeqIO.to_dict(SeqIO.parse(fasta_file, 'fasta'))
    for sequence_id, sequence_record in sequences.items():
        if search_string in sequence_record.seq:
            print(f"Match found in sequence with ID: {sequence_id}")
            print(f"Sequence Description: {sequence_record.description}")
            print(f"Matched Substring: {search_string}")
            print("=" * 30)
            return True
    print(f"No match found for substring: {search_string}")
    return False

def find_matching_position(sequence, search_string):
    position = sequence.find(search_string)
    return position

fasta_file = 'P04217.fasta'
search_442688365 = 'TDGEGALSEPSATVTIEELAAPPPPVLMHHGESSQVLHPGNK'
match_sequence(fasta_file, search_442688365)

sequence = SeqIO.to_dict(SeqIO.parse(fasta_file, 'fasta'))
id = 'sp|P04217|A1BG_HUMAN'
amino_acid_sequence = sequence[id].seq
match_position = find_matching_position(amino_acid_sequence, search_442688365)
print(f"Match found at position: {match_position}")
 

so that the matched position is found at position 185.