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add ICM datatype for glimmer

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This commit is contained in:
Anthony Bretaudeau
2017-11-20 11:41:06 +01:00
parent 2a0c7114df
commit 1cfdf85879
2 changed files with 28 additions and 0 deletions
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config/datatypes_conf.xml.sample
+2
View File
@@ -491,6 +491,7 @@
<!-- Annotation Datatypes -->
<datatype extension="snaphmm" type="galaxy.datatypes.annotation:SnapHmm" display_in_upload="true" />
<datatype extension="augustus" type="galaxy.datatypes.annotation:Augustus" display_in_upload="true" />
<datatype extension="icm" type="galaxy.datatypes.binary:ICM" display_in_upload="true"/>
<!-- MSA Datatypes -->
<datatype extension="hmm2" type="galaxy.datatypes.msa:Hmmer2" display_in_upload="true" />
<datatype extension="hmm3" type="galaxy.datatypes.msa:Hmmer3" display_in_upload="true" />
@@ -682,6 +683,7 @@
<sniffer type="galaxy.datatypes.binary:Fast5ArchiveGz" />
<sniffer type="galaxy.datatypes.binary:Fast5ArchiveBz2" />
<sniffer type="galaxy.datatypes.binary:Fast5Archive" />
<sniffer type="galaxy.datatypes.annotation:ICM" />
<sniffer type="galaxy.datatypes.annotation:Augustus" />
<sniffer type="galaxy.datatypes.triples:Rdf"/>
<sniffer type="galaxy.datatypes.blast:BlastXml"/>
lib/galaxy/datatypes/binary.py
+26
View File
@@ -1792,6 +1792,32 @@ class DMND(Binary):
Binary.register_sniffable_binary_format("dmnd", "dmnd", DMND)
class ICM(Binary):
"""
Class describing an ICM (interpolated context model) file, used by Glimmer
"""
file_ext = "icm"
edam_data = "data_0950"
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = "Binary ICM (interpolated context model) file"
dataset.blurb = nice_size(dataset.get_size())
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
def sniff(self, dataset):
line = open(dataset).readline()
if '>ver = ' in line and 'len = ' in line and 'depth = ' in line and 'periodicity =' in line and 'nodes = ' in line:
return True
return False
Binary.register_sniffable_binary_ext("icm", "icm", ICM)
if __name__ == '__main__':
import doctest
doctest.testmod(sys.modules[__name__])