Merge pull request #9592 from nsoranzo/release_19.09_add_paf_gfa_datatypes (7adb2a38) · Commits · NDIP / Galaxy

lib/galaxy/config/sample/datatypes_conf.xml.sample

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		@@ -17,6 +17,8 @@
		<datatype extension="anvio_structure_db" type="galaxy.datatypes.anvio:AnvioStructureDB" display_in_upload="false" />
		<datatype extension="anvio_variability" type="galaxy.datatypes.tabular:TSV" display_in_upload="false" subclass="true" />
		<datatype extension="arff" type="galaxy.datatypes.text:Arff" mimetype="text/plain" display_in_upload="true"/>
		<datatype extension="paf" type="galaxy.datatypes.text:Paf" mimetype="text/plain" display_in_upload="true"/>
		<datatype extension="gfa1" type="galaxy.datatypes.text:Gfa1" mimetype="text/plain" display_in_upload="true"/>
		<datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true"/>
		<datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true"/>
		<datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format. Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/>
		@@ -376,6 +378,7 @@
		<display file="igb/wig.xml"/>
		</datatype>
		<datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="true"/>
		<datatype extension="odgi" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs self index used by odgi."/>
		<datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="true"/>
		<datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="true"/>
		<datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" display_in_upload="true">
		@@ -876,6 +879,7 @@
		<sniffer type="galaxy.datatypes.interval:Gff"/>
		<sniffer type="galaxy.datatypes.interval:Gff3"/>
		<sniffer type="galaxy.datatypes.tabular:Pileup"/>
		<sniffer type="galaxy.datatypes.text:Paf"/>
		<sniffer type="galaxy.datatypes.interval:Interval"/>
		<sniffer type="galaxy.datatypes.tabular:Sam"/>
		<sniffer type="galaxy.datatypes.data:Newick"/>

lib/galaxy/datatypes/test/A-3105.paf

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lib/galaxy/datatypes/test/big.gfa1

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		# Downloaded from https://github.com/sjackman/gfalint/blob/master/examples/big1.gfa
		H VN:Z:1.0
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lib/galaxy/datatypes/text.py

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		@@ -730,3 +730,84 @@ class IQTree(Text):
		False
		"""
		return file_prefix.startswith("IQ-TREE")


		@build_sniff_from_prefix
		class Paf(Text):
		"""
		PAF: a Pairwise mApping Format

		https://github.com/lh3/miniasm/blob/master/PAF.md
		"""
		file_ext = "paf"

		def sniff_prefix(self, file_prefix):
		"""
		>>> from galaxy.datatypes.sniff import get_test_fname
		>>> fname = get_test_fname('A-3105.paf')
		>>> Paf().sniff(fname)
		True
		"""
		found_valid_lines = False
		for line in iter_headers(file_prefix, "\t"):
		if len(line) < 12:
		return False
		for i in (1, 2, 3, 6, 7, 8, 9, 10, 11):
		int(line[i])
		if line[4] not in ('+', '-'):
		return False
		if not (0 <= int(line[11]) <= 255):
		return False
		# Check that the optional columns after the 12th contain SAM-like typed key-value pairs
		for i in range(12, len(line)):
		if len(line[i].split(':')) != 3:
		return False
		found_valid_lines = True
		return found_valid_lines


		@build_sniff_from_prefix
		class Gfa1(Text):
		"""
		Graphical Fragment Assembly (GFA) 1.0

		http://gfa-spec.github.io/GFA-spec/GFA1.html
		"""
		file_ext = "gfa1"

		def sniff_prefix(self, file_prefix):
		"""
		>>> from galaxy.datatypes.sniff import get_test_fname
		>>> fname = get_test_fname('big.gfa1')
		>>> Gfa1().sniff(fname)
		True
		"""
		found_valid_lines = False
		for line in iter_headers(file_prefix, "\t"):
		if line[0].startswith('#'):
		continue
		if line[0] == 'H':
		return len(line) == 2 and line[1] == 'VN:Z:1.0'
		elif line[0] == 'S':
		if len(line) < 3:
		return False
		elif line[0] == 'L':
		if len(line) < 6:
		return False
		for i in (2, 4):
		if line[i] not in ('+', '-'):
		return False
		elif line[0] == 'C':
		if len(line) < 7:
		return False
		for i in (2, 4):
		if line[i] not in ('+', '-'):
		return False
		int(line[5])
		elif line[0] == 'P':
		if len(line) < 4:
		return False
		else:
		return False
		found_valid_lines = True
		return found_valid_lines

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