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Source code for galaxy.datatypes.metacyto

MetaCyto analysis datatypes.

import logging

from galaxy.datatypes.sniff import FilePrefix
from galaxy.datatypes.tabular import Tabular

log = logging.getLogger(__name__)

[docs]class mStats(Tabular): """Class describing the table of cluster statistics output from MetaCyto""" file_ext = "metacyto_stats.txt"
[docs] def sniff_prefix(self, file_prefix: FilePrefix): """Quick test on file headings""" if file_prefix.startswith("fcs_files\tcluster_id\tlabel\tfcs_names"): header_line = file_prefix.string_io().readline() if header_line.strip().split("\t")[-1] == 'fraction': return True elif file_prefix.truncated and file_prefix.string_io().read() == header_line: return True return False
[docs]class mSummary(Tabular): """Class describing the summary table output by MetaCyto after FCS preprocessing""" file_ext = "metacyto_summary.txt"
[docs] def sniff_prefix(self, file_prefix: FilePrefix): return file_prefix.startswith('study_id\tantibodies\tfilenames')