Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.datatypes.microarrays

import logging

from galaxy.datatypes import data
from galaxy.datatypes.binary import Cel  # noqa: F401
from galaxy.datatypes.data import get_file_peek
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.sniff import (
    build_sniff_from_prefix,
    get_headers
)

log = logging.getLogger(__name__)


[docs]class GenericMicroarrayFile(data.Text): """ Abstract class for most of the microarray files. """ MetadataElement(name="version_number", default="1.0", desc="Version number", readonly=True, visible=True, optional=True, no_value="1.0") MetadataElement(name="file_format", default="ATF", desc="File format", readonly=True, visible=True, optional=True, no_value="ATF") MetadataElement(name="number_of_optional_header_records", default=1, desc="Number of optional header records", readonly=True, visible=True, optional=True, no_value=1) MetadataElement(name="number_of_data_columns", default=1, desc="Number of data columns", readonly=True, visible=True, optional=True, no_value=1) MetadataElement(name="file_type", default="GenePix", desc="File type", readonly=True, visible=True, optional=True, no_value="GenePix") MetadataElement(name="block_count", default=1, desc="Number of blocks described in the file", readonly=True, visible=True, optional=True, no_value=1) MetadataElement(name="block_type", default=0, desc="Type of block", readonly=True, visible=True, optional=True, no_value=0)
[docs] def set_peek(self, dataset, is_multi_byte=False): if not dataset.dataset.purged: if dataset.metadata.block_count == 1: dataset.blurb = "{} {}: Format {}, 1 block, {} headers and {} columns".format(dataset.metadata.file_type, dataset.metadata.version_number, dataset.metadata.file_format, dataset.metadata.number_of_optional_header_records, dataset.metadata.number_of_data_columns) else: dataset.blurb = "{} {}: Format {}, {} blocks, {} headers and {} columns".format(dataset.metadata.file_type, dataset.metadata.version_number, dataset.metadata.file_format, dataset.metadata.block_count, dataset.metadata.number_of_optional_header_records, dataset.metadata.number_of_data_columns) dataset.peek = get_file_peek(dataset.file_name) else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk'
[docs] def get_mime(self): return 'text/plain'
[docs]@build_sniff_from_prefix class Gal(GenericMicroarrayFile): """ Gal File format described at: http://mdc.custhelp.com/app/answers/detail/a_id/18883/#gal """ edam_format = "format_3829" edam_data = "data_3110" file_ext = "gal"
[docs] def sniff_prefix(self, file_prefix): """ Try to guess if the file is a Gal file. >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname('test.gal') >>> Gal().sniff(fname) True >>> fname = get_test_fname('test.gpr') >>> Gal().sniff(fname) False """ headers = get_headers(file_prefix, sep="\t", count=3) return "ATF" in headers[0][0] and "GenePix ArrayList" in headers[2][0]
[docs] def set_meta(self, dataset, **kwd): """ Set metadata for Gal file. """ super().set_meta(dataset, **kwd) headers = get_headers(dataset.file_name, sep="\t", count=5) dataset.metadata.file_format = headers[0][0] dataset.metadata.version_number = headers[0][1] dataset.metadata.number_of_optional_header_records = int(headers[1][0]) dataset.metadata.number_of_data_columns = int(headers[1][1]) dataset.metadata.file_type = headers[2][0].strip().strip('"').split("=")[1] if "BlockCount" in headers[3][0]: dataset.metadata.block_count = int(headers[3][0].strip().strip('"').split("=")[1]) if "BlockType" in headers[4][0]: dataset.metadata.block_type = int(headers[4][0].strip().strip('"').split("=")[1])
[docs]@build_sniff_from_prefix class Gpr(GenericMicroarrayFile): """ Gpr File format described at: http://mdc.custhelp.com/app/answers/detail/a_id/18883/#gpr """ edam_format = "format_3829" edam_data = "data_3110" file_ext = "gpr"
[docs] def sniff_prefix(self, file_prefix): """ Try to guess if the file is a Gpr file. >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname('test.gpr') >>> Gpr().sniff(fname) True >>> fname = get_test_fname('test.gal') >>> Gpr().sniff(fname) False """ headers = get_headers(file_prefix, sep="\t", count=3) return "ATF" in headers[0][0] and "GenePix Results" in headers[2][0]
[docs] def set_meta(self, dataset, **kwd): """ Set metadata for Gpr file. """ super().set_meta(dataset, **kwd) headers = get_headers(dataset.file_name, sep="\t", count=5) dataset.metadata.file_format = headers[0][0] dataset.metadata.version_number = headers[0][1] dataset.metadata.number_of_optional_header_records = int(headers[1][0]) dataset.metadata.number_of_data_columns = int(headers[1][1]) dataset.metadata.file_type = headers[2][0].strip().strip('"').split("=")[1]