From bfe1e40480a61029652ecb0b5391b7b71ca5640c Mon Sep 17 00:00:00 2001 From: anton Date: Fri, 24 Apr 2015 16:18:20 -0400 Subject: [PATCH 1/2] Added default indexing for bcc files --- lib/galaxy/datatypes/binary.py | 35 +++++++++++++++++++++++++++++++++- 1 file changed, 34 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py index 3d6f6e0e1e4..b596ec61ff7 100644 --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -423,11 +423,12 @@ class Bam( Binary ): Binary.register_sniffable_binary_format("bam", "bam", Bam) - class Bcf( Binary): """Class describing a BCF file""" file_ext = "bcf" + MetadataElement( name="bcf_index", desc="BCF Index File", param=metadata.FileParameter, file_ext="csi", readonly=True, no_value=None, visible=False, optional=True ) + def sniff( self, filename ): # BCF is compressed in the BGZF format, and must not be uncompressed in Galaxy. # The first 3 bytes of any bcf file is 'BCF', and the file is binary. @@ -439,6 +440,38 @@ class Bcf( Binary): except: return False + def set_meta( self, dataset, overwrite = True, **kwd ): + """ Creates the index for the BCF file. """ + # These metadata values are not accessible by users, always overwrite + index_file = dataset.metadata.bcf_index + if not index_file: + index_file = dataset.metadata.spec['bcf_index'].param.new_file( dataset = dataset ) + # Create the bcf index + ##$ bcftools index + ##Usage: bcftools index + + dataset_symlink = os.path.join( os.path.dirname( index_file.file_name ), + '__dataset_%d_%s' % ( dataset.id, os.path.basename( index_file.file_name ) ) ) + os.symlink( dataset.file_name, dataset_symlink ) + + stderr_name = tempfile.NamedTemporaryFile( prefix = "bcf_index_stderr" ).name + command = [ 'bcftools', 'index', dataset_symlink ] + proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) ) + exit_code = proc.wait() + shutil.move( dataset_symlink + '.csi', index_file.file_name ) + + stderr = open( stderr_name ).read().strip() + if stderr: + if exit_code != 0: + os.unlink( stderr_name ) #clean up + raise Exception, "Error Setting BCF Metadata: %s" % stderr + else: + print stderr + dataset.metadata.bcf_index = index_file + # Remove temp file + os.unlink( stderr_name ) + + Binary.register_sniffable_binary_format("bcf", "bcf", Bcf) From 41343e4b41116e36648f00b09b82417d71bf714a Mon Sep 17 00:00:00 2001 From: anton Date: Tue, 28 Apr 2015 13:45:33 -0400 Subject: [PATCH 2/2] Added test for bcf index creation. --- lib/galaxy/datatypes/binary.py | 1 - test-data/bcf_index_metadata_test.bcf | Bin 0 -> 12492 bytes test-data/bcf_index_metadata_test.txt | 1 + test/functional/tools/metadata_bcf.xml | 16 ++++++++++++++++ test/functional/tools/sample_datatypes_conf.xml | 1 + test/functional/tools/samples_tool_conf.xml | 1 + 6 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 test-data/bcf_index_metadata_test.bcf create mode 100644 test-data/bcf_index_metadata_test.txt create mode 100644 test/functional/tools/metadata_bcf.xml diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py index b596ec61ff7..b2bd21c1533 100644 --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -471,7 +471,6 @@ class Bcf( Binary): # Remove temp file os.unlink( stderr_name ) - Binary.register_sniffable_binary_format("bcf", "bcf", Bcf) diff --git a/test-data/bcf_index_metadata_test.bcf b/test-data/bcf_index_metadata_test.bcf new file mode 100644 index 0000000000000000000000000000000000000000..244518810e7296e2eb26f52c765c9ffcd8a3cf4e GIT binary patch literal 12492 zcmV;-Ff-2|iwFb&00000{{{d;LjnN*9kpExd{gDwZ$UuZyi^B>4$X?JsJ)z9PLe{= zLrO!HT7*bpZa|u(Z7@wjk^)7%4)sGf*ruY>xv7J}+|;RKZqq3^FPqBdP=?>s>2%J^ zPu)II8Q(tOdvj^>oYUvLIX&ln-OnLyp8xZ_&-;Ha?Wduz*lZQ;WD)@UZ2j-|4(WTK^3i^p9=DjQ8_ zT&Ykd6OGi?x3?~C5oQs|a59mN_2wnT`gkY(JiTn9>pM| zmSj94Q6#9I;WBQ6jHe{y_KC7rRS_Sk1{rTjMp0!|A#NBh<1xti$}*xP%EaNrWxU2Y z6-q*~+bt^|1sRafC?o~)J?pBs@fl0hu9K_q&7UXK@%GSWdT z^Fi>)iqEYeb1NDNA(j~-NN!n_eTdgZBPGNVCwzkJRy=Nu;zmx0B~o}r(dU*#%swM2 z#1bn!Ucuv$6wDPyR){595cWx4pBFRFNDHY%3sokra7&nZMp{TES}0yo@}cu94NDLu 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b/test/functional/tools/metadata_bcf.xml new file mode 100644 index 00000000000..396a8bd7abd --- /dev/null +++ b/test/functional/tools/metadata_bcf.xml @@ -0,0 +1,16 @@ + + file "${input_bcf.metadata.bcf_index}" > "${output_of_input_metadata}" + + + + + + + + + + + + + + diff --git a/test/functional/tools/sample_datatypes_conf.xml b/test/functional/tools/sample_datatypes_conf.xml index ffde6ae5be9..28cb5ff2df7 100644 --- a/test/functional/tools/sample_datatypes_conf.xml +++ b/test/functional/tools/sample_datatypes_conf.xml @@ -12,5 +12,6 @@ + \ No newline at end of file diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml index c4c86f5272f..143e9043a3f 100644 --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -16,6 +16,7 @@ +