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Source code for galaxy.datatypes.ngsindex

NGS indexes
import logging
import os

from .metadata import MetadataElement
from .text import Html

log = logging.getLogger(__name__)

[docs]class BowtieIndex(Html): """ base class for BowtieIndex is subclassed by BowtieColorIndex and BowtieBaseIndex """ MetadataElement(name="base_name", desc="base name for this index set", default='galaxy_generated_bowtie_index', set_in_upload=True, readonly=True) MetadataElement(name="sequence_space", desc="sequence_space for this index set", default='unknown', set_in_upload=True, readonly=True) composite_type = 'auto_primary_file' allow_datatype_change = False
[docs] def generate_primary_file(self, dataset=None): """ This is called only at upload to write the html file cannot rename the datasets here - they come with the default unfortunately """ return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>'
[docs] def regenerate_primary_file(self, dataset): """ cannot do this until we are setting metadata """ bn = dataset.metadata.base_name flist = os.listdir(dataset.extra_files_path) rval = ['<html><head><title>Files for Composite Dataset %s</title></head><p/>Comprises the following files:<p/><ul>' % (bn)] for i, fname in enumerate(flist): sfname = os.path.split(fname)[-1] rval.append('<li><a href="{}">{}</a>'.format(sfname, sfname)) rval.append('</ul></html>') with open(dataset.file_name, 'w') as f: f.write("\n".join(rval)) f.write('\n')
[docs] def set_peek(self, dataset, is_multi_byte=False): if not dataset.dataset.purged: dataset.peek = "Bowtie index file (%s)" % (dataset.metadata.sequence_space) dataset.blurb = "%s space" % (dataset.metadata.sequence_space) 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 "Bowtie index file"
[docs]class BowtieColorIndex(BowtieIndex): """ Bowtie color space index """ MetadataElement(name="sequence_space", desc="sequence_space for this index set", default='color', set_in_upload=True, readonly=True) file_ext = 'bowtie_color_index'
[docs]class BowtieBaseIndex(BowtieIndex): """ Bowtie base space index """ MetadataElement(name="sequence_space", desc="sequence_space for this index set", default='base', set_in_upload=True, readonly=True) file_ext = 'bowtie_base_index'