Source code for galaxy.datatypes.flow

Flow analysis datatypes.

import logging

from galaxy.datatypes.binary import Binary
from galaxy.datatypes.protocols import DatasetProtocol
from galaxy.datatypes.sniff import (
from . import data

log = logging.getLogger(__name__)

[docs]@build_sniff_from_prefix class FCS(Binary): """Class describing an FCS binary file""" file_ext = "fcs"
[docs] def set_peek(self, dataset: DatasetProtocol, **kwd) -> None: if not dataset.dataset.purged: dataset.peek = "Binary FCS file" dataset.blurb = data.nice_size(dataset.get_size()) else: dataset.peek = "file does not exist" dataset.blurb = "file purged from disk"
[docs] def display_peek(self, dataset: DatasetProtocol) -> str: try: return dataset.peek except Exception: return "Binary FCS file"
[docs] def sniff_prefix(self, file_prefix: FilePrefix) -> bool: """ Checking if the file is in FCS format. Should read FCS2.0, FCS3.0 and FCS3.1 Based on flowcore: """ content = file_prefix.contents_header_bytes[:42].decode() version = content[:6] if version not in ["FCS2.0", "FCS3.0", "FCS3.1"]: return False if content[6:10] != " ": return False # we only need to check ioffs 2 to 5 int(content[10:42].replace(" ", "")) return True