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Add IdeasPre datatype subclassed from Rgenetics

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greg
2018-02-02 09:22:10 -05:00
parent 60561c2030
commit b5945ad3e3
2 changed files with 70 additions and 0 deletions
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config/datatypes_conf.xml.sample
+3
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@@ -675,6 +675,9 @@
<datatype extension="allegro_ihaplo" type="galaxy.datatypes.tabular:Tabular" />
<datatype extension="allegro_descent" type="galaxy.datatypes.tabular:Tabular" />
<datatype extension="allegro_fparam" type="galaxy.datatypes.genetics:AllegroLOD" />
<!-- IDEAS datatypes -->
<datatype extension="ideaspre" type="galaxy.datatypes.genetics:IdeasPre" display_in_upload="true"/>
<!-- End IDEAS datatypes -->
</registration>
<sniffers>
<!--
lib/galaxy/datatypes/genetics.py
+67
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@@ -518,6 +518,73 @@ class Snptest(Rgenetics):
file_ext = "snptest"
class IdeasPre(Rgenetics):
"""
This datatype defines the input format required by IDEAS:
https://academic.oup.com/nar/article/44/14/6721/2468150
The IDEAS preprocessor tool produces an output using this
format. The extra_files_path of the primary input dataset
contains the following files and directories.
- chromosome_windows.txt (optional)
- chromosomes.bed (optional)
- IDEAS_input_config.txt
- compressed archived tmp directory containing a number of compressed bed files.
"""
MetadataElement(name="base_name", desc="Base name for this dataset", default='IDEASData', readonly=True, set_in_upload=True)
MetadataElement(name="chrom_bed", desc="Bed file specifying window positions", default=None, readonly=True)
MetadataElement(name="chrom_windows", desc="Chromosome window positions", default=None, readonly=True)
MetadataElement(name="input_config", desc="IDEAS input config", default=None, readonly=True)
MetadataElement(name="tmp_archive", desc="Compressed archive of compressed bed files", default=None, readonly=True)
composite_type = 'auto_primary_file'
allow_datatype_change = False
file_ext = 'ideaspre'
def __init__(self, **kwd):
Html.__init__(self, **kwd)
self.add_composite_file('chromosome_windows.txt', description='Chromosome window positions', is_binary=False, optional=True)
self.add_composite_file('chromosomes.bed', description='Bed file specifying window positions', is_binary=False, optional=True)
self.add_composite_file('IDEAS_input_config.txt', description='IDEAS input config', is_binary=False)
self.add_composite_file('tmp.tar.gz', description='Compressed archive of compressed bed files', is_binary=True)
def set_meta(self, dataset, **kwd):
Html.set_meta(self, dataset, **kwd)
for fname in os.listdir(dataset.extra_files_path):
if fname.startswith("chromosomes"):
dataset.metadata.chrom_bed = os.path.join(dataset.extra_files_path, fname)
elif fname.startswith("chromosome_windows"):
dataset.metadata.chrom_windows = os.path.join(dataset.extra_files_path, fname)
elif fname.startswith("IDEAS_input_config"):
dataset.metadata.input_config = os.path.join(dataset.extra_files_path, fname)
elif fname.startswith("tmp"):
dataset.metadata.tmp_archive = os.path.join(dataset.extra_files_path, fname)
self.regenerate_primary_file(dataset)
def generate_primary_file(self, dataset=None):
rval = ['<html><head></head><body>']
rval.append('<h3>Files prepared for IDEAS</h3>')
rval.append('<ul>')
for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
fn = composite_name
rval.append('<li><a href="%s>%s</a></li>' % (fn, fn))
rval.append('</ul></body></html>\n')
return "\n".join(rval)
def regenerate_primary_file(self, dataset):
# Cannot do this until we are setting metadata.
rval = ['<html><head></head><body>']
rval.append('<h3>Files prepared for IDEAS</h3>')
rval.append('<ul>')
for fname in os.listdir(dataset.extra_files_path):
fn = os.path.split(fname)[-1]
rval.append('<li><a href="%s">%s</a></li>' % (fn, fn))
rval.append('</ul></body></html>')
with open(dataset.file_name, 'w') as f:
f.write("\n".join(rval))
f.write('\n')
class Pheno(Tabular):
"""
base class for pheno files