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Source code for galaxy.datatypes.flow

Flow analysis datatypes.

import logging

from galaxy.datatypes.binary import Binary
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): 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): try: return dataset.peek except Exception: return "Binary FCS file"
[docs] def sniff_prefix(self, file_prefix: FilePrefix): """ Checking if the file is in FCS format. Should read FCS2.0, FCS3.0 and FCS3.1 Based on flowcore: https://github.com/RGLab/flowCore/blob/27141b792ad65ae8bd0aeeef26e757c39cdaefe7/R/IO.R#L667 """ 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