Source code for galaxy.datatypes.qualityscore

"""
Qualityscore class
"""
import logging

from galaxy.datatypes.protocols import DatasetProtocol
from galaxy.datatypes.sniff import (
    build_sniff_from_prefix,
    FilePrefix,
)
from . import data

log = logging.getLogger(__name__)


[docs]class QualityScore(data.Text): """ until we know more about quality score formats """ edam_data = "data_2048" edam_format = "format_3606" file_ext = "qual"
[docs]@build_sniff_from_prefix class QualityScoreSOLiD(QualityScore): """ until we know more about quality score formats """ edam_format = "format_3610" file_ext = "qualsolid"
[docs] def sniff_prefix(self, file_prefix: FilePrefix) -> bool: """ >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname( 'sequence.fasta' ) >>> QualityScoreSOLiD().sniff( fname ) False >>> fname = get_test_fname( 'sequence.qualsolid' ) >>> QualityScoreSOLiD().sniff( fname ) True """ fh = file_prefix.string_io() readlen = None goodblock = 0 for line in fh: line = line.strip() if not line.startswith("#"): # first non-empty non-comment line if line.startswith(">"): line = fh.readline().strip() if line == "" or line.startswith(">"): return False try: [int(x) for x in line.split()] if not readlen: readlen = len(line.split()) assert len(line.split()) == readlen # SOLiD reads should be of the same length except Exception: return False goodblock += 1 if goodblock > 10: return True else: return False return goodblock > 0
[docs] def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None: if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize: dataset.metadata.data_lines = None return return QualityScore.set_meta(self, dataset, overwrite=overwrite, **kwd)
[docs]@build_sniff_from_prefix class QualityScore454(QualityScore): """ until we know more about quality score formats """ edam_format = "format_3611" file_ext = "qual454"
[docs] def sniff_prefix(self, file_prefix: FilePrefix) -> bool: """ >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname( 'sequence.fasta' ) >>> QualityScore454().sniff( fname ) False >>> fname = get_test_fname( 'sequence.qual454' ) >>> QualityScore454().sniff( fname ) True """ fh = file_prefix.string_io() for line in fh: line = line.strip() if line and not line.startswith("#"): # first non-empty non-comment line if line.startswith(">"): line = fh.readline().strip() if line == "" or line.startswith(">"): break try: [int(x) for x in line.split()] except Exception: return False return True else: break # we found a non-empty line, but it's not a header return False
[docs]class QualityScoreSolexa(QualityScore): """ until we know more about quality score formats """ edam_format = "format_3608" file_ext = "qualsolexa"
[docs]class QualityScoreIllumina(QualityScore): """ until we know more about quality score formats """ edam_format = "format_3609" file_ext = "qualillumina"