comparison scripts/validate_fasta.py @ 23:2891385d6ace draft

planemo upload for repository https://github.com/usegalaxy-au/tools-au commit b347c6ccc82b14fcbff360b3357050d1d43e3ef5-dirty

22:3f188450ca4f

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


class FastaLoader:
    def __init__(self, fasta_path: str):
        """Initialize from FASTA file."""

    def validate_length(self):
        """Confirm whether sequence length is valid."""
        fasta = self.fasta_list[0]
        if self.min_length:
            if len(fasta.aa_seq) < self.min_length:
                raise ValueError(
                    'Error encountered validating FASTA:\n Sequence too short'
                    f' ({len(fasta.aa_seq)}AA).'
                    f' Minimum length is {self.min_length}AA.')
        if self.max_length:
            if len(fasta.aa_seq) > self.max_length:
                raise ValueError(
                    'Error encountered validating FASTA:\n'
                    f' Sequence too long ({len(fasta.aa_seq)}AA).'
                    f' Maximum length is {self.max_length}AA.')

    def validate_alphabet(self):
        """Confirm whether the sequence conforms to IUPAC codes.

        If not, report the offending character and its position.
        """
        fasta = self.fasta_list[0]
        for i, char in enumerate(fasta.aa_seq.upper()):
            if char not in self.iupac_characters:
                raise ValueError(
                    'Error encountered validating FASTA:\n Invalid amino acid'
                    f' found at pos {i}: "{char}"')

    def validate_x(self):
        """Check for X bases."""
        fasta = self.fasta_list[0]
        for i, char in enumerate(fasta.aa_seq.upper()):
            if char == 'X':
                raise ValueError(
                    'Error encountered validating FASTA:\n Unsupported AA code'
                    f' "X" found at pos {i}')

    def __init__(self) -> None:
        self.line_wrap = 60

    def write(self, fasta: Fasta):
        header = fasta.header
        seq = self.format_sequence(fasta.aa_seq)
        sys.stdout.write(header + '\n')
        sys.stdout.write(seq)

    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

            fw.write(fas)

        sys.stderr.write("Validated FASTA sequence(s):\n\n")
        for fas in clean_fastas:
            sys.stderr.write(fas.header + '\n')
            sys.stderr.write(fas.aa_seq + '\n\n')

    except ValueError as exc:
        sys.stderr.write(f"{exc}\n\n")
        raise exc

23:2891385d6ace

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


class FastaLoader:
    def __init__(self, fasta_path: str):
        """Initialize from FASTA file."""

    def validate_length(self):
        """Confirm whether sequence length is valid."""
        fasta = self.fasta_list[0]
        if self.min_length:
            if len(fasta.sequence) < self.min_length:
                raise ValueError(
                    'Error encountered validating FASTA:\n Sequence too short'
                    f' ({len(fasta.sequence)}AA).'
                    f' Minimum length is {self.min_length}AA.')
        if self.max_length:
            if len(fasta.sequence) > self.max_length:
                raise ValueError(
                    'Error encountered validating FASTA:\n'
                    f' Sequence too long ({len(fasta.sequence)}AA).'
                    f' Maximum length is {self.max_length}AA.')

    def validate_alphabet(self):
        """Confirm whether the sequence conforms to IUPAC codes.

        If not, report the offending character and its position.
        """
        fasta = self.fasta_list[0]
        for i, char in enumerate(fasta.sequence.upper()):
            if char not in self.iupac_characters:
                raise ValueError(
                    'Error encountered validating FASTA:\n Invalid amino acid'
                    f' found at pos {i}: "{char}"')

    def validate_x(self):
        """Check for X bases."""
        fasta = self.fasta_list[0]
        for i, char in enumerate(fasta.sequence.upper()):
            if char == 'X':
                raise ValueError(
                    'Error encountered validating FASTA:\n Unsupported AA code'
                    f' "X" found at pos {i}')

    def __init__(self) -> None:
        self.line_wrap = 60

    def write(self, fasta: Fasta):
        header = fasta.header
        seq = self.format_sequence(fasta.sequence)
        sys.stdout.write(header + '\n')
        sys.stdout.write(seq)

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


def main():
    # load fasta file

            fw.write(fas)

        sys.stderr.write("Validated FASTA sequence(s):\n\n")
        for fas in clean_fastas:
            sys.stderr.write(fas.header + '\n')
            sys.stderr.write(fas.sequence + '\n\n')

    except ValueError as exc:
        sys.stderr.write(f"{exc}\n\n")
        raise exc