mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-28 02:58:18 +08:00
Move PlantTribes datatypes to a separate file, will replace PR 3999
This commit is contained in:
Greg Von Kuster
@@ -602,11 +602,18 @@
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<datatype extension="maskinfo-asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" subclass="true" display_in_upload="true" />
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<datatype extension="pssm-asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" subclass="true" display_in_upload="true" />
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<!-- PlantTribes datatypes -->
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<datatype extension="ptalign" type="galaxy.datatypes.text:PlantTribesMultipleSequenceAlignment" />
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<datatype extension="ptortho" type="galaxy.datatypes.text:PlantTribesOrtho" />
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<datatype extension="ptorthocs" type="galaxy.datatypes.text:PlantTribesOrthoCodingSequence" />
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<datatype extension="pttree" type="galaxy.datatypes.text:PlantTribesPhylogeneticTree" />
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<datatype extension="smat" type="galaxy.datatypes.text:Smat" display_in_upload="true" />
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<datatype extension="ptalign" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignment" />
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<datatype extension="ptalignca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentCodonAlignment" />
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<datatype extension="ptaligntrimmed" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmed" />
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<datatype extension="ptaligntrimmedca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment" />
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<datatype extension="ptalignfiltered" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFiltered" />
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<datatype extension="ptalignfilteredca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment" />
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<datatype extension="ptortho" type="galaxy.datatypes.plant_tribes:PlantTribesOrtho" />
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<datatype extension="ptorthocs" type="galaxy.datatypes.plant_tribes:PlantTribesOrthoCodingSequence" />
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<datatype extension="ptphylip" type="galaxy.datatypes.plant_tribes:PlantTribesPhylip" />
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<datatype extension="pttgf" type="galaxy.datatypes.plant_tribes:PlantTribesTargetedGeneFamilies" />
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<datatype extension="pttree" type="galaxy.datatypes.plant_tribes:PlantTribesPhylogeneticTree" />
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<datatype extension="smat" type="galaxy.datatypes.plant_tribes:Smat" display_in_upload="true" />
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</registration>
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<sniffers>
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<!--
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@@ -0,0 +1,249 @@
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import logging
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import os
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import re
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import tempfile
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from galaxy.datatypes.data import get_file_peek, Text
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from galaxy.datatypes.metadata import MetadataElement, MetadataParameter
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from galaxy.datatypes.text import Html
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from galaxy.util import nice_size
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log = logging.getLogger(__name__)
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class Smat(Text):
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file_ext = "smat"
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def display_peek(self, dataset):
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try:
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return dataset.peek
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except:
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return "ESTScan scores matrices (%s)" % (nice_size(dataset.get_size()))
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def set_peek(self, dataset, is_multi_byte=False):
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if not dataset.dataset.purged:
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dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
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dataset.blurb = "ESTScan scores matrices"
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else:
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dataset.peek = 'file does not exist'
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dataset.blurb = 'file purged from disc'
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def sniff(self, filename):
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"""
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The use of ESTScan implies the creation of scores matrices which
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reflect the codons preferences in the studied organisms. The
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ESTScan package includes scripts for generating these files. The
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output of these scripts consists of the matrices, one for each
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isochor, and which look like this:
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FORMAT: hse_4is.conf CODING REGION 6 3 1 s C+G: 0 44
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-1 0 2 -2
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2 1 -8 0
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>>> from galaxy.datatypes.sniff import get_test_fname
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>>> fname = get_test_fname('test_space.txt')
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>>> Smat().sniff(fname)
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False
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>>> fname = get_test_fname('test_tab.bed')
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>>> Smat().sniff(fname)
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False
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>>> fname = get_test_fname('1.smat')
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>>> Smat().sniff(fname)
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True
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"""
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line_no = 0
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with open(filename, "r") as fh:
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line_no += 1
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if line_no > 10000:
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return True
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line = fh.readline(500)
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if line_no == 1 and not line.startswith('FORMAT'):
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# The first line is always the start of a format section.
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return False
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if not line.startswith('FORMAT'):
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if line.find('\t') >= 0:
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# Smat files are not tabular.
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return False
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items = line.split()
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if len(items) != 4:
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return False
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for item in items:
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# Make sure each item is an integer.
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if re.match(r"[-+]?\d+$", item) is None:
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return False
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return True
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class PlantTribes(Html):
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"""
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PlantTribes abstract class.
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"""
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composite_type = 'basic'
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MetadataElement(name="num_files", default=0, desc="Number of files in files_path directory", param=MetadataParameter, readonly=True, visible=False, no_value=0)
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def display_data(self, trans, data, preview=False, filename=None, to_ext=None, **kwd):
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file_path = trans.app.object_store.get_filename(data.dataset, extra_dir='dataset_%s_files' % data.dataset.id, alt_name=filename)
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if os.path.isdir(file_path):
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fh = tempfile.NamedTemporaryFile(delete=False)
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fn = fh.name
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dir_items = sorted(os.listdir(file_path))
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# Directories can only contain either files or directories, but not both.
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item_path = os.path.join(file_path, dir_items[0])
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if os.path.isdir(item_path):
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header = 'Directories'
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else:
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header = 'Datasets'
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base_path, item_name = os.path.split(file_path)
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fh.write('<html><head><h3>Directory %s contents: %d items</h3></head>\n' % (item_name, len(dir_items)))
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fh.write('<body><p/><table cellpadding="2">\n')
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fh.write('<tr><b>%s</b></tr>\n' % header)
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for index, fname in enumerate(dir_items):
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if index % 2 == 0:
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bgcolor = '#D8D8D8'
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else:
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bgcolor = '#FFFFFF'
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# Can't have an href link here because there is no route
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# defined for files contained within multiple subdirectory
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# levels of the primary dataset. Something like this is
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# close, but not quite correct:
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# href = url_for(controller='dataset', action='display',
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# dataset_id=trans.security.encode_id(data.dataset.id),
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# preview=preview, filename=fname, to_ext=to_ext)
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fh.write('<tr bgcolor="%s"><td>%s</td></tr>\n' % (bgcolor, fname))
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fh.write('</table></body></html>\n')
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fh.close()
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return open(fn)
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else:
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return super(PlantTribes, self).display_data(trans, data, preview=preview, filename=filename, to_ext=to_ext, **kwd)
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def set_meta(self, dataset, overwrite=True, **kwd):
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try:
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efp = dataset.extra_files_path
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if os.path.exists(efp):
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dataset.metadata.num_files = len(os.listdir(efp))
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except Exception as e:
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log.warning("set_meta fname: %s %s" % (dataset.file_name if dataset and dataset.file_name else 'Unkwown', str(e)))
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class PlantTribesOrtho(PlantTribes):
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"""
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PlantTribes sequences classified into precomputed, orthologous gene family
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clusters.
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"""
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file_ext = "ptortho"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesOrtho, self).set_peek(dataset, is_multi_byte=is_multi_byte)
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dataset.blurb = "Proteins orthogroup fasta files: %d items" % dataset.metadata.num_files
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class PlantTribesOrthoCodingSequence(PlantTribes):
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"""
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PlantTribes sequences classified into precomputed, orthologous gene family
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clusters and corresponding coding sequences.
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"""
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file_ext = "ptorthocs"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesOrthoCodingSequence, self).set_peek(dataset, is_multi_byte=is_multi_byte)
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dataset.blurb = "Protein and coding sequences orthogroup fasta files: %d items" % dataset.metadata.num_files
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class PlantTribesTargetedGeneFamilies(PlantTribes):
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"""
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PlantTribes targeted gene families.
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"""
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file_ext = "pttgf"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesTargetedGeneFamilies, self).set_peek(dataset, is_multi_byte=is_multi_byte)
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dataset.blurb = "Targeted gene families"
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class PlantTribesPhylogeneticTree(PlantTribes):
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"""
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PlantTribes multiple sequence alignments and inferred maximum likelihood
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phylogenies for orthogroups.
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"""
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file_ext = "pttree"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesPhylogeneticTree, self).set_peek(dataset, is_multi_byte=is_multi_byte)
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dataset.blurb = "Phylogenetic trees: %d items" % dataset.metadata.num_files
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class PlantTribesPhylip(PlantTribes):
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"""
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PlantTribes orthogroup phylip multiple sequence alignments.
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"""
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file_ext = "ptphylip"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesPhylip, self).set_peek(dataset, is_multi_byte=is_multi_byte)
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dataset.blurb = "Orthogroup phylip multiple sequence alignments: %d items" % dataset.metadata.num_files
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class PlantTribesMultipleSequenceAlignment(PlantTribes):
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"""
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PlantTribes multiple sequence alignments.
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"""
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file_ext = "ptalign"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesMultipleSequenceAlignment, self).set_peek(dataset, is_multi_byte=is_multi_byte)
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dataset.blurb = "Proteins orthogroup alignments: %d items" % dataset.metadata.num_files
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class PlantTribesMultipleSequenceAlignmentCodonAlignment(PlantTribes):
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"""
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PlantTribes multiple sequence alignments with codon alignments.
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"""
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file_ext = "ptalignca"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesMultipleSequenceAlignmentCodonAlignment, self).set_peek(dataset, is_multi_byte=is_multi_byte)
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dataset.blurb = "Protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
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class PlantTribesMultipleSequenceAlignmentTrimmed(PlantTribes):
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"""
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PlantTribes trimmed multiple sequence alignments.
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"""
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file_ext = "ptaligntrimmed"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesMultipleSequenceAlignmentTrimmed, self).set_peek(dataset, is_multi_byte=is_multi_byte)
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dataset.blurb = "Trimmed proteins orthogroup alignments: %d items" % dataset.metadata.num_files
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class PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment(PlantTribes):
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"""
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PlantTribes trimmed multiple sequence alignments with codon alignments.
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"""
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file_ext = "ptaligntrimmedca"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment, self).set_peek(dataset, is_multi_byte=is_multi_byte)
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dataset.blurb = "Trimmed protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
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class PlantTribesMultipleSequenceAlignmentFiltered(PlantTribes):
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"""
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PlantTribes filtered multiple sequence alignments.
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"""
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file_ext = "ptalignfiltered"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesMultipleSequenceAlignmentFiltered, self).set_peek(dataset, is_multi_byte=is_multi_byte)
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dataset.blurb = "Filtered proteins orthogroup alignments: %d items" % dataset.metadata.num_files
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class PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment(PlantTribes):
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"""
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PlantTribes filtered multiple sequence alignments with codon alignments.
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"""
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file_ext = "ptalignfilteredca"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment, self).set_peek(dataset, is_multi_byte=is_multi_byte)
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dataset.blurb = "Filtered protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
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@@ -542,113 +542,3 @@ class SnpSiftDbNSFP( Text ):
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else:
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dataset.peek = 'file does not exist'
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dataset.blurb = 'file purged from disc'
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class Smat(Text):
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file_ext = "smat"
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def display_peek(self, dataset):
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try:
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return dataset.peek
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except:
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return "ESTScan scores matrices (%s)" % (nice_size(dataset.get_size()))
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def set_peek(self, dataset, is_multi_byte=False):
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if not dataset.dataset.purged:
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dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
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dataset.blurb = "ESTScan scores matrices"
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else:
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dataset.peek = 'file does not exist'
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dataset.blurb = 'file purged from disc'
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def sniff(self, filename):
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"""
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The use of ESTScan implies the creation of scores matrices which
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reflect the codons preferences in the studied organisms. The
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ESTScan package includes scripts for generating these files. The
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output of these scripts consists of the matrices, one for each
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isochor, and which look like this:
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FORMAT: hse_4is.conf CODING REGION 6 3 1 s C+G: 0 44
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-1 0 2 -2
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2 1 -8 0
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>>> from galaxy.datatypes.sniff import get_test_fname
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>>> fname = get_test_fname('test_space.txt')
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>>> Smat().sniff(fname)
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False
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>>> fname = get_test_fname('test_tab.bed')
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>>> Smat().sniff(fname)
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False
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>>> fname = get_test_fname('1.smat')
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>>> Smat().sniff(fname)
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True
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"""
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line_no = 0
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with open(filename, "r") as fh:
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line_no += 1
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if line_no > 10000:
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return True
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line = fh.readline(500)
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if line_no == 1 and not line.startswith('FORMAT'):
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# The first line is always the start of a format section.
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return False
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if not line.startswith('FORMAT'):
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if line.find('\t') >= 0:
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# Smat files are not tabular.
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return False
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items = line.split()
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if len(items) != 4:
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return False
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for item in items:
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# Make sure each item is an integer.
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if re.match(r"[-+]?\d+$", item) is None:
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return False
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return True
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class PlantTribesOrtho(Html):
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"""
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PlantTribes sequences classified into precomputed, orthologous gene family
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clusters.
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"""
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file_ext = "ptortho"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesOrtho, self).set_peek(dataset, is_multi_byte=is_multi_byte)
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dataset.blurb = "PlantTribes gene family clusters: %d files" % dataset.metadata.data_lines
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class PlantTribesOrthoCodingSequence(Html):
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"""
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PlantTribes sequences classified into precomputed, orthologous gene family
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clusters and corresponding coding sequences.
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"""
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file_ext = "ptorthocs"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesOrthoCodingSequence, self).set_peek(dataset, is_multi_byte=is_multi_byte)
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dataset.blurb = "PlantTribes gene family clusters with corresponding coding sequences: %d files" % dataset.metadata.data_lines
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class PlantTribesPhylogeneticTree(Html):
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"""
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PlantTribes multiple sequence alignments and inferred maximum likelihood
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phylogenies for orthogroups.
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"""
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file_ext = "pttree"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesPhylogeneticTree, self).set_peek(dataset, is_multi_byte=is_multi_byte)
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dataset.blurb = "PlantTribes phylogenetic trees: %d files" % dataset.metadata.data_lines
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class PlantTribesMultipleSequenceAlignment(Html):
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"""
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PlantTribes multiple sequence alignments for orthogroups.
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"""
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file_ext = "ptalign"
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def set_peek(self, dataset, is_multi_byte=False):
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super(PlantTribesMultipleSequenceAlignment, self).set_peek(dataset, is_multi_byte=is_multi_byte)
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dataset.blurb = "PlantTribes multiple sequence alignments: %d files" % dataset.metadata.data_lines
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