rjchallis
commented
2 years ago I think the problem here is that you are missing the dataset name from the end of your blobtools filter command and blobtools2 is interpreting the second fasta filename as the BlobDir name. You should only need to specify the input fasta filename so with a BlobDir named ASSEMBLY_NAME, your command would look like:
/Users/maysonlin/Documents/blobtoolkit/blobtools2/blobtools filter --query-string "http://localhost:8001/view/dataset/ASSEMBLY_NAME/blob?bestsumorder_phylum--Keys=3#Filters" --fasta /Users/maysonlin/Documents/BTK_TUTORIAL/FILES/Pregina.p_ctg.purged.fa ASSEMBLY_NAMEHope this helps
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Hi, I have issue filtering based upon taxonomic contigs. Here is the error messages I received:
WARN: Skipping field 'bestsumorder_phylum', not present in dataset Traceback (most recent call last): File "/Users/maysonlin/Documents/blobtoolkit/blobtools2/lib/filter.py", line 381, in <module> main() File "/Users/maysonlin/Documents/blobtoolkit/blobtools2/lib/filter.py", line 250, in main indices = [index for index, value in enumerate(identifiers.values)] AttributeError: 'bool' object has no attribute 'values'My script:
/Users/maysonlin/Documents/blobtoolkit/blobtools2/blobtools filter --query-string "http://localhost:8001/view/dataset/ASSEMBLY_NAME/blob?bestsumorder_phylum--Keys=3#Filters" --fasta /Users/maysonlin/Documents/BTK_TUTORIAL/FILES/Pregina.p_ctg.purged.fa /Users/maysonlin/Documents/BTK_TUTORIAL/FILES/Pregina.p_ctg_filtered.purged.faI also tried using
--param bestsumorder_phylum--Keys=Probacteriaand--json /Users/maysonlin/Downloads/ASSEMBLY_NAME.current.json, still similar messages:WARN: Skipping field 'bestsumorder_class', not present in dataset Traceback (most recent call last): File "/Users/maysonlin/Documents/blobtoolkit/blobtools2/lib/filter.py", line 381, in <module> main() File "/Users/maysonlin/Documents/blobtoolkit/blobtools2/lib/filter.py", line 250, in main indices = [index for index, value in enumerate(identifiers.values)] AttributeError: 'bool' object has no attribute 'values'&
Traceback (most recent call last): File "/Users/maysonlin/Documents/blobtoolkit/blobtools2/lib/filter.py", line 381, in <module> main() File "/Users/maysonlin/Documents/blobtoolkit/blobtools2/lib/filter.py", line 250, in main indices = [index for index, value in enumerate(identifiers.values)] AttributeError: 'bool' object has no attribute 'values'here is my "identifiers.json" looks like:
{"id":"current","datasetId":"ASSEMBLY_NAME","search":"view","params":{"bestsumorder_class--Active":"true","bestsumorder_phylum--Keys":"1"},"identifiers":["ptg000001l_1","ptg000002l_1","ptg000004l_1","ptg000005l_1","ptg000006l_1","ptg000007l_1","ptg000008l_1","ptg000009l_1","ptg000010l_1","ptg000012l_1","ptg000013l_1","ptg000014l_1","ptg000015l_1","ptg000016l_1","ptg000017l_1","ptg000018l_1","ptg000019l_1","ptg000020l_1","ptg000021l_1","ptg000022l_1","ptg000023l_1","ptg000024l_1","ptg000025l_1","ptg000026l_1","ptg000027l_1","ptg000028l_1","ptg000029l_1","ptg000030l_1","ptg000031l_1","ptg000033l_1","ptg000034l_1","ptg000035l_1","ptg000036l_1","ptg000037l_1","ptg000038l_1","ptg000039l_1","ptg000040l_1","ptg000041l_1","ptg000042l_1","ptg000043l_1","ptg000044l_1","ptg000045l_1","ptg000046l_1","ptg000049l_1","ptg000050l_1","ptg000051l_1","ptg000052l_1","ptg000053l_1","ptg000054l_1","ptg000055l_1","ptg000057l_1","ptg000058l_1","ptg000059l_1","ptg000061l_1","ptg000062l_1","ptg000063l_1","ptg000064l_1","ptg000065l_1","ptg000066l_1","ptg000067l_1","ptg000068l_1","ptg000069l_1","ptg000070l_1","ptg000071l_1","ptg000072l_1","ptg000073l_1","ptg000074l_1","ptg000075l_1","ptg000076l_1","ptg000077l_1","ptg000078l_1","ptg000079l_1","ptg000080l_1","ptg000081l_1","ptg000082l_1","ptg000083l_1","ptg000085l_1","ptg000086l_1","ptg000087l_1","ptg000088l_1","ptg000089l_1","ptg000090l_1","ptg000091l_1","ptg000092l_1","ptg000093l_1","ptg000095l_1","ptg000097l_1","ptg000099l_1","ptg000100l_1","ptg000102l_1","ptg000104l_1","ptg000105l_1","ptg000106l_1","ptg000107l_1","ptg000108l_1","ptg000110l_1","ptg000112l_1","ptg000113l_1","ptg000114l_1","ptg000116l_1","ptg000117l_1","ptg000120l_1","ptg000121l_1","ptg000125l_1","ptg000126l_1","ptg000127l_1","ptg000128l_1","ptg000130l_1","ptg000131l_1","ptg000132l_1","ptg000133l_1","ptg000136l_1","ptg000137l_1","ptg000138l_1","ptg000139l_1","ptg000144l_1","ptg000145l_1","ptg000146l_1","ptg000147l_1","ptg000148l_1","ptg000150l_1","ptg000151l_1","ptg000161l_1","ptg000165l_1","ptg000175l_1","ptg000185l_1","ptg000187l_1","ptg000191l_1","ptg000236l_1","ptg000291l_1","ptg000326l_1"],"summaryStats":{"hits":{"total":{"span":534549832,"count":131,"n50":8201560,"l50":17,"n90":1945816,"l90":68},"Arthropoda":{"count":129,"span":534356185,"n50":8201560},"Proteobacteria":{"count":0,"span":0,"n50":0},"no-hit":{"count":2,"span":193647,"n50":154887}},"taxonomy":{"taxid":7380,"lineage":"Eukaryota; Metazoa; Arthropoda; Insecta; Diptera; Calliphoridae; Phormia; Phormia regina","target":"Arthropoda","targetRank":"phylum"},"baseComposition":{"at":0.731,"gc":0.269,"n":0},"busco":{"diptera_odb10":{"c":3263,"d":8,"m":11,"f":11,"t":3285,"s":3255,"string":"C:99.3%[S:99.1%,D:0.2%],F:0.3%,M:0.3%,n:3285"}},"stats":{"noHit":0.000362,"target":1,"spanOverN50":65.2},"readMapping":{}}}& bestsumorder_phylum.json:
{ "values": [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 1, 0, 0, 0, 2, 1, 0, 1, 1, 0 ], "keys": [ "Arthropoda", "Proteobacteria", "no-hit" ] }Hope these info helps solve the problems, I also tried to adjust
length--Min=, still same message withfilter.pyline problem. I updated blobtoolkit withgit clone https://github.com/blobtoolkit/blobtools2;, still the same issues with them all. I doubt if it'sfilter.pyproblem, but any suggestion can help, thank you for your time!