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API.tests.csv
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68 lines (68 loc) · 12.6 KB
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bf0461f5474cd711525dcd104452005b https://api.mg-rast.org/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt tab delimited annotated sequence stream
339b8286827d5051c693e51049ee5cf6 curl -X POST -d '{"source":"SwissProt","type":"organism","data":["000821a2e2f63df1a3873e4b280002a8","15bf1950bd9867099e72ea6516e3d602"]}' "https://api.mg-rast.org/annotation/sequence/mgm4447943.3" tab delimited annotated sequence stream
4978084e1997239e5ea92c873262585e https://api.mg-rast.org/annotation/similarity/mgm4447943.3?identity=80&type=function&source=KO tab delimited blast m8 with annotation
68b42706feff1891cc279d2b34c83ea7 curl -X POST -d '{"source":"KO","type":"function","data":["000821a2e2f63df1a3873e4b280002a8","15bf1950bd9867099e72ea6516e3d602"]}' "https://api.mg-rast.org/annotation/sequence/mgm4447943.3" tab delimited blast m8 with annotation
093f18b3f9fdf63756d185ca3eb4600a https://api.mg-rast.org/compute/alphadiversity/mgm4447943.3?level=order Calculate alpha diversity value for given ID and taxon level.
be43b392342e558d8285fda7ce6304d3 https://api.mg-rast.org/compute/rarefaction/mgm4447943.3?level=order Calculate rarefaction x-y coordinates for given ID and taxon level.
68e5cdee454154209011533a7cc5723e https://api.mg-rast.org/compute/blast/mgm4447943.3?md5=15bf1950bd9867099e72ea6516e3d602 Produce NCBI-BLAST sequence alinments for given md5sum and its hits.
08a8e4cd32d6f24f22775e83254557a3 curl -X POST -d '{"columns": ["mgm4441619.3","mgm4441656.4","mgm4441680.3","mgm4441681.3"], "rows": ["Eukaryota","Bacteria","Archaea"], "data": [[135,410,848,1243],[4397,6529,71423,204413],[1422,2156,874,1138]]}' "https://api.mg-rast.org/compute/normalize" Calculate normalized values for given input data.
352f914894421f3fc8369da8b05ca764 curl -X POST -d '{"distance":"euclidean","columns": ["mgm4441619.3","mgm4441656.4","mgm4441680.3","mgm4441681.3"], "rows": ["Eukaryota","Bacteria","Archaea"], "data": [[135,410,848,1243],[4397,6529,71423,204413],[1422,2156,874,1138]]}' "https://api.mg-rast.org/compute/distance" Calculate a distance matrix for given input data.
1cc8a59993211d6b8f8aaf30f9b36aff curl -X POST -d '{"raw":0,"cluster":"mcquitty","columns": ["mgm4441619.3","mgm4441656.4","mgm4441680.3","mgm4441681.3"], "rows": ["Eukaryota","Bacteria","Archaea"], "data": [[135,410,848,1243],[4397,6529,71423,204413],[1422,2156,874,1138]]}' "https://api.mg-rast.org/compute/heatmap" Calculate a dendrogram for given input data.
7e57d184dd8e9688f4f69e903dd78039 curl -X POST -d '{"raw":1,"distance":"euclidean","columns": ["mgm4441619.3","mgm4441656.4","mgm4441680.3","mgm4441681.3"], "rows": ["Eukaryota","Bacteria","Archaea"], "data": [[135,410,848,1243],[4397,6529,71423,204413],[1422,2156,874,1138]]}' "https://api.mg-rast.org/compute/pcoa" Calculate a PCoA for given input data.
854ae4e0208dbc8ac43d23d04d9d8ea8 https://api.mg-rast.org/darkmatter/mgm4447943.3? Returns a darkmatter sequence file.
a1f7d6aa8a46de535b50f25a228bbc57 https://api.mg-rast.org/download/mgm4447943.3?file=350.1 Returns a single sequence file.
0ad289490c101f5d4a34b76e3cf17dd4 https://api.mg-rast.org/download/history/mgm4447943.3 Summary of MG-RAST analysis-pipeline workflow and commands.
475ea223c2861425b17473d42c5aab8f https://api.mg-rast.org/download/mgm4447943.3?stage=650 Returns a list of sets of sequence files for the given id.
c93ca883230dbbca572572124767bd03 curl -X GET -H "auth: auth_key" "https://api.mg-rast.org/inbox" lists the contents of the user inbox
0da1888480b0709036726fec8d547773 curl -X GET -H "auth: auth_key" "https://api.mg-rast.org/inbox/pending?queued&completed" view status of AWE inbox actions
fd3ce4cad9fbb586184601df43e59a5b curl -X POST -H "auth: auth_key" -F "upload=@sequences.fastq" "https://api.mg-rast.org/inbox" receives user inbox data upload, auto-uncompress if has .gz or .bz2 file extension
8cf68cacf8a4010ad82a3fcc7b094b53 curl -X DELETE -H "auth: auth_key" "https://api.mg-rast.org/inbox/cfb3d9e1-c9ba-4260-95bf-e410c57b1e49" delete indicated file from inbox
48e721ca63c3610650285c1e1fe6de8e curl -X GET -H "auth: auth_key" -F "format=tar" "https://api.mg-rast.org/inbox/upload/cfb3d9e1-c9ba-4260-95bf-e410c57b1e49" unpacks an archive upload into mutlple inbox files. supports: .zip, .tar, .tar.gz, .tar.bz2
4e7cb41ce81012d43762466725fc65c9 curl -X GET -H "auth: auth_key" "https://api.mg-rast.org/inbox/info/cfb3d9e1-c9ba-4260-95bf-e410c57b1e49" get basic file info - returns results and updates shock node
94c8286b3e5003f03e1ea3ea70bcc8f2 curl -X GET -H "auth: auth_key" "https://api.mg-rast.org/inbox/validate/cfb3d9e1-c9ba-4260-95bf-e410c57b1e49" validate metadata spreadsheet in inbox
925d23448291db8cd558c04f26adf94c curl -X GET -H "auth: auth_key" "https://api.mg-rast.org/inbox/stats/cfb3d9e1-c9ba-4260-95bf-e410c57b1e49" runs sequence stats on file in user inbox - submits AWE job
a4527dd2910b4bd523947240f20d3fca curl -X GET -H "auth: auth_key" "https://api.mg-rast.org/inbox/cancel/cfb3d9e1-c9ba-4260-95bf-e410c57b1e49" cancel (delete) given AWE job ID
5dcf850e81902a6e19861158ebeeec49 curl -X POST -H "auth: auth_key" "https://api.mg-rast.org/inbox/rename" rename indicated file from inbox
e70762df20c7be49a5f742a91ab6f0cf curl -X POST -H "auth: auth_key" -F "sff_file=cfb3d9e1-c9ba-4260-95bf-e410c57b1e49" "https://api.mg-rast.org/inbox/sff2fastq" create fastq file from sff file - submits AWE job
77cc651f99544db3fe87afd017f43cfa curl -X POST -H "auth: auth_key" -F "seq_file=cfb3d9e1-c9ba-4260-95bf-e410c57b1e49" -F "barcode_file=cfb3d9e1-c9ba-4260-95bf-e410c57b1e49" "https://api.mg-rast.org/inbox/demultiplex" demultiplex seq file with barcode file - submits AWE job
a234d523384cae184f53ec5d561e28d8 curl -X POST -H "auth: auth_key" -F "retain=1" -F "pair_file_1=cfb3d9e1-c9ba-4260-95bf-e410c57b1e49" -F "pair_file_2=cfb3d9e1-c9ba-4260-95bf-e410c57b1e49" "https://api.mg-rast.org/inbox/pairjoin" merge overlapping paired-end fastq files - submits AWE job
7502b6ba11a891b18291be501bb44672 curl -X POST -H "auth: auth_key" -F "pair_file_1=cfb3d9e1-c9ba-4260-95bf-e410c57b1e49" -F "pair_file_2=cfb3d9e1-c9ba-4260-95bf-e410c57b1e49" -F "index_file=cfb3d9e1-c9ba-4260-95bf-e410c57b1e49" "https://api.mg-rast.org/inbox/pairjoin_demultiplex" merge overlapping paired-end fastq files and demultiplex based on index file - submits AWE job
14ff2d38c41218f3af58b2004a5d69a2 https://api.mg-rast.org/library?limit=20&order=name Returns a set of data matching the query criteria.
77b4d2434b8f73ff6848e966f239402c https://api.mg-rast.org/library/mgl52924?verbosity=full Returns a single data object.
63db592a6ed698b4d53d5252491e6f5c https://api.mg-rast.org/m5nr/ontology?source=Subsystems&min_level=level3 Return functional hierarchy
530de3b8d27c7229184f7b4931f0efd9 https://api.mg-rast.org/m5nr/taxonomy?filter=Bacteroidetes&filter_level=phylum&min_level=genus Return organism hierarchy
bef098bdd304902d730cab5a79a1f191 https://api.mg-rast.org/m5nr/sources Return all sources in M5NR
3f462bbac13117870755eead0dc46d64 https://api.mg-rast.org/m5nr/accession/YP_003268079.1 Return annotation of given source protein ID
cbd270785474a895912f3737f1cc7b25 https://api.mg-rast.org/m5nr/alias/GI:485708283 Return annotations for alias IDs containing the given text
a00503660af17c9ab8a505c2dff4a0af https://api.mg-rast.org/m5nr/md5/000821a2e2f63df1a3873e4b280002a8?source=InterPro Return annotation(s) or sequence of given md5sum (M5NR ID)
45c7e500a0bf8585f96da513807d6a2d https://api.mg-rast.org/m5nr/function/sulfatase?source=GenBank Return annotations for function names containing the given text
be4fe029618e91007d6758acc3f6b851 https://api.mg-rast.org/m5nr/organism/akkermansia?source=KEGG Return annotations for organism names containing the given text
e7d349855e898967f0efb647fc0e8462 https://api.mg-rast.org/m5nr/sequence/MSTAITRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTGGQTSMAFAMEGETQQQQGEATIQRIVRQASKLRVVFATDEEIAAHEARLDLVQKKGGSCLWRA?source=TrEMBL Return annotation(s) for md5sum (M5NR ID) of given sequence
57873ec56edbca158a5e32984a69f535 curl -X POST -d '{"order":"function","data":["YP_003268079.1","COG1764"]}' "https://api.mg-rast.org/m5nr/accession" Return annotations of given source protein IDs
757f6029083aa957a0614f386bba2c09 curl -X POST -d '{"order":"function","data":["GI:485708283","fig|511145.6.peg.216"]}' "https://api.mg-rast.org/m5nr/alias" Return annotations for aliases containing the given texts
5ade830aaf8947985af71d44e1952d16 curl -X POST -d '{"source":"InterPro","data":["000821a2e2f63df1a3873e4b280002a8","15bf1950bd9867099e72ea6516e3d602"]}' "https://api.mg-rast.org/m5nr/md5" Return annotations or sequences of given md5sums (M5NR ID)
4737573e4564fda6a5783742ca88db4c curl -X POST -d '{"source":"GenBank","limit":50,"data":["sulfatase","phosphatase"]}' "https://api.mg-rast.org/m5nr/function" Return annotations for function names containing the given texts
9d1b020daf035e015741ae38eaa4d504 curl -X POST -d '{"source":"KEGG","order":"accession","data":["akkermansia","yersinia"]}' "https://api.mg-rast.org/m5nr/organism" Return annotations for organism names containing the given texts
9b7bc182a5851760d64822e3da629fbb curl -X POST -d '{"source":"GenBank","order":"source","data":["MAGENHQWQGSIL","MAGENHQWQGSIL"]}' "https://api.mg-rast.org/m5nr/sequence" Return annotations for md5s (M5NR ID) of given sequences
94477516fd2a92c2e1a63b78c2f749ab https://api.mg-rast.org/matrix/organism?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&group_level=family&source=RefSeq&evalue=15 Returns a BIOM object.
dc50f6494186a9686e4aba71532cd125 https://api.mg-rast.org/matrix/function?id=mgm4447943.3&id=mgm4447192.3&id=mgm4447102.3&group_level=level3&source=Subsystems&identity=80 Returns a BIOM object.
afca8786a7ba38d62c54efc0e0f47755 https://api.mg-rast.org/metadata/template Returns static template for metadata object relationships and types
5f0e7489e011a9ec5c40918acb32e754 https://api.mg-rast.org/metadata/cv?label=country Returns static controlled vocabularies used in metadata. By default returns all CVs at latest version. If label and version options used, returns those specific values.
7d7bce8d921ba0083806b0aa6aafbe19 https://api.mg-rast.org/metadata/ontology?name=biome&version=2017-04-15 Returns static ontology used in metadata for the given name and version.
eb28e5343d589f377ec80bcd95c63f93 https://api.mg-rast.org/metadata/version?label=biome Returns all versions available for given ontology.
88aed515f7afbd8c9038c71a2b088eb6 https://api.mg-rast.org/metadata/view/biome Returns list of unique metadata values submitted by users for given label
c44c8b35b39a74ddc9e20ff501d7d67d https://api.mg-rast.org/metadata/export/mgp128 Returns full nested metadata for a project in same format as template, or metadata for a single metagenome.
c9ae49e087db2722acb6e25ca9a29132 curl -X POST -F "metagenome=mgm12345" -F "metagenome=mgm67890" -F "upload=@metadata.xlsx" "https://api.mg-rast.org/metadata/import" Create project with given metadata spreadsheet and metagenome IDs, either upload or shock node
2c603ef4c925f2b5b0110d677193669a curl -X POST -F "project=mgp123" -F "upload=@metadata.xlsx" "https://api.mg-rast.org/metadata/update" Update project with given metadata spreadsheet and metagenome IDs, either upload or shock node
1f241ea51e9d8688cc41b4cde83fd0b0 curl -X POST -F "upload=@metadata.xlsx" "https://api.mg-rast.org/metadata/validate" Validate given metadata spreadsheet, either upload or shock node
17dc47fbbb7d58c69fd69c9e996d9a94 https://api.mg-rast.org/metadata/validate?category=sample&label=material&value=soil Validate given metadata value
eb494bafc265fe1ecd27703324278476 https://api.mg-rast.org/metagenome?limit=20&order=name Returns a set of data matching the query criteria.
0c9e1784736939f8eea4df3ee19e60b8 https://api.mg-rast.org/metagenome/mgm4447943.3?verbosity=metadata Returns a single data object.
59a9013eb264ffdc2c5d1ab80b487a71 https://api.mg-rast.org/profile/mgm4447943.3?source=RefSeq&format=biom Submits profile creation
d5cb4930331ec889e859fa815fdcc48b https://api.mg-rast.org/project?limit=20&order=name Returns a set of data matching the query criteria.
d754c6a2f59125b6f5b06562eb0cfc3b https://api.mg-rast.org/project/mgp128?verbosity=full Returns a single data object.
b9e674e88feb451d3bdcb549756ef850 https://api.mg-rast.org/sample?limit=20&order=name Returns a set of data matching the query criteria.
cc9ab29aac803a9025381f15a4ffb394 https://api.mg-rast.org/sample/mgs25823?verbosity=full Returns a single data object.
458942635efb2b87477ccd0ba9565a1c https://api.mg-rast.org/search?material=saline water Elastic search
2fc0943b297f5b1c1beedbff1b971a6f https://api.mg-rast.org/validation/template/ Checks if the referenced JSON structure is a valid template
84167878cdbb204047cc950e6fdb7b13 https://api.mg-rast.org/validation/data/?template= Returns a single data object.