comparison validate_fasta.py @ 8:ca90d17ff51b draft

"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 03537aada92b5fff565ff48dd47c81462c5df47e"

7:eb085b3dbaf8

"""Validate input FASTA sequence."""

import re
import sys
import argparse
from typing import List, TextIO


class Fasta:
    def __init__(self, header_str: str, seq_str: str):
        self.header = header_str

        # self.validate_x()

    def validate_num_seqs(self) -> None:
        """Assert that only one sequence has been provided."""
        if len(self.fasta_list) > 1:
            raise ValueError(
                'Error encountered validating FASTA:\n'
                f' More than 1 sequence detected ({len(self.fasta_list)}).'
                ' Please use single FASTA sequence as input.')
        elif len(self.fasta_list) == 0:
            raise ValueError(
                'Error encountered validating FASTA:\n'
                ' input file has no FASTA sequences')

    def format_sequence(self, aa_seq: str):
        formatted_seq = ''
        for i in range(0, len(aa_seq), self.line_wrap):
            formatted_seq += aa_seq[i: i + self.line_wrap] + '\n'
        return formatted_seq


def main():
    # load fasta file
    try:

8:ca90d17ff51b

"""Validate input FASTA sequence."""

import re
import sys
import argparse
from typing import List


class Fasta:
    def __init__(self, header_str: str, seq_str: str):
        self.header = header_str

        # self.validate_x()

    def validate_num_seqs(self) -> None:
        """Assert that only one sequence has been provided."""
        if len(self.fasta_list) > 1:
            sys.stderr.write(
                'WARNING: More than 1 sequence detected.'
                ' Using first FASTA sequence as input.\n')
            self.fasta_list = self.fasta_list[:1]
        elif len(self.fasta_list) == 0:
            raise ValueError(
                'Error encountered validating FASTA:\n'
                ' input file has no FASTA sequences')

    def format_sequence(self, aa_seq: str):
        formatted_seq = ''
        for i in range(0, len(aa_seq), self.line_wrap):
            formatted_seq += aa_seq[i: i + self.line_wrap] + '\n'
        return formatted_seq.upper()


def main():
    # load fasta file
    try: