StephenFordham

def pattern_check(pattern):
    answer = pattern.upper()
    if (len(answer) < 4 or len(answer) > 8) or re.search('[^AGCT]', answer):
            raise argparse.ArgumentTypeError('A valid restriction enzyme must be entered: \n'
                                             '1. Between 4-8 bases long \n2. Comprise of the nucleotides A, G, C and T')
    return answer

StephenFordham

arg_parse.py -p AAGGCGC AGAGGGAT -i E.coli_genome.fasta -c -2
arg_parse.py -i E.coli_genome.fasta -c -2 -p AAGGCGC AGAGGGAT
arg_parse.py  --pattern AAGGCGC AGAGGGAT -i E.coli_genome.fasta --count_no 50
arg_parse.py  --input_filename E.coli_genome.fasta -c 50 -p AAGGCGC AGAGGGAT

StephenFordham

result = []
for seq in args.pattern:
    for x in re.findall(seq, DNA):
        result.append(x)

restriction_enzyme = collections.Counter(result)

StephenFordham

import re
import collections

import argparse
parser = argparse.ArgumentParser(description='Finding restriction sites in DNA sequences')


def count_valid(count_no):
    num = int(count_no)
    if num < 1:

StephenFordham

parser.add_argument('-p',
                    '--pattern',
                    help='Enter the pattern of the restriction enzyme',
                    type=pattern_check,
                    nargs='*')

StephenFordham

def count_valid(count_no):
    num = int(count_no)
    if num < 1:
        raise argparse.ArgumentTypeError('The count has to be an integer above 0')
    return num

StephenFordham

parser.add_argument('-c',
                    '--count_no',
                    help='count number to be specified',
                    type=count_valid,
                    default=0)

StephenFordham

import re
import collections

import argparse
parser = argparse.ArgumentParser(description='Finding restriction sites in DNA sequences')


def count_valid(count_no):
    num = int(count_no)
    if num < 1:

StephenFordham

import pandas as pd

StephenFordham

Blast = pd.read_csv('SPECIES_BLAST_DATA.CSV')
print(Blast.head())
print(Blast.columns)
print(Blast.shape)