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Support NCBI sequence_report.jsonl as input for CollectAlternateContigNames #945
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Can you post the full JSON? Also, can you point me to where it lives on FTP? I don't see it here: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.26_GRCh38/ |
I am not sure that those files exist as physical files or that they are always generated on the fly by the REST API by NCBI https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/rest-api/# Full file: {"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"1","gcCount":"103674491","gcPercent":41.5,"genbankAccession":"CM000663.2","length":248956422,"refseqAccession":"NC_000001.11","role":"assembled-molecule","ucscStyleName":"chr1","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"2","gcCount":"101284083","gcPercent":40.0,"genbankAccession":"CM000664.2","length":242193529,"refseqAccession":"NC_000002.12","role":"assembled-molecule","ucscStyleName":"chr2","unlocalizedCount":2}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"3","gcCount":"91922884","gcPercent":39.5,"genbankAccession":"CM000665.2","length":198295559,"refseqAccession":"NC_000003.12","role":"assembled-molecule","ucscStyleName":"chr3","unlocalizedCount":1}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"4","gcCount":"76972588","gcPercent":38.0,"genbankAccession":"CM000666.2","length":190214555,"refseqAccession":"NC_000004.12","role":"assembled-molecule","ucscStyleName":"chr4","unlocalizedCount":1}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"5","gcCount":"93718374","gcPercent":39.0,"genbankAccession":"CM000667.2","length":181538259,"refseqAccession":"NC_000005.10","role":"assembled-molecule","ucscStyleName":"chr5","unlocalizedCount":1}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"6","gcCount":"68907366","gcPercent":39.5,"genbankAccession":"CM000668.2","length":170805979,"refseqAccession":"NC_000006.12","role":"assembled-molecule","ucscStyleName":"chr6"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"7","gcCount":"70693857","gcPercent":40.5,"genbankAccession":"CM000669.2","length":159345973,"refseqAccession":"NC_000007.14","role":"assembled-molecule","ucscStyleName":"chr7"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"8","gcCount":"76166139","gcPercent":40.0,"genbankAccession":"CM000670.2","length":145138636,"refseqAccession":"NC_000008.11","role":"assembled-molecule","ucscStyleName":"chr8"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"9","gcCount":"52944769","gcPercent":41.0,"genbankAccession":"CM000671.2","length":138394717,"refseqAccession":"NC_000009.12","role":"assembled-molecule","ucscStyleName":"chr9","unlocalizedCount":4}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"10","gcCount":"59342366","gcPercent":41.0,"genbankAccession":"CM000672.2","length":133797422,"refseqAccession":"NC_000010.11","role":"assembled-molecule","ucscStyleName":"chr10"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"11","gcCount":"70204082","gcPercent":41.5,"genbankAccession":"CM000673.2","length":135086622,"refseqAccession":"NC_000011.10","role":"assembled-molecule","ucscStyleName":"chr11","unlocalizedCount":1}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"12","gcCount":"58038673","gcPercent":40.5,"genbankAccession":"CM000674.2","length":133275309,"refseqAccession":"NC_000012.12","role":"assembled-molecule","ucscStyleName":"chr12"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"13","gcCount":"38619357","gcPercent":38.5,"genbankAccession":"CM000675.2","length":114364328,"refseqAccession":"NC_000013.11","role":"assembled-molecule","ucscStyleName":"chr13"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"14","gcCount":"45815948","gcPercent":40.5,"genbankAccession":"CM000676.2","length":107043718,"refseqAccession":"NC_000014.9","role":"assembled-molecule","ucscStyleName":"chr14","unlocalizedCount":8}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"15","gcCount":"46742416","gcPercent":42.0,"genbankAccession":"CM000677.2","length":101991189,"refseqAccession":"NC_000015.10","role":"assembled-molecule","ucscStyleName":"chr15","unlocalizedCount":1}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"16","gcCount":"48251436","gcPercent":44.5,"genbankAccession":"CM000678.2","length":90338345,"refseqAccession":"NC_000016.10","role":"assembled-molecule","ucscStyleName":"chr16","unlocalizedCount":1}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"17","gcCount":"46714680","gcPercent":45.0,"genbankAccession":"CM000679.2","length":83257441,"refseqAccession":"NC_000017.11","role":"assembled-molecule","ucscStyleName":"chr17","unlocalizedCount":3}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"18","gcCount":"40613699","gcPercent":39.5,"genbankAccession":"CM000680.2","length":80373285,"refseqAccession":"NC_000018.10","role":"assembled-molecule","ucscStyleName":"chr18"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"19","gcCount":"32693605","gcPercent":47.5,"genbankAccession":"CM000681.2","length":58617616,"refseqAccession":"NC_000019.10","role":"assembled-molecule","ucscStyleName":"chr19"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"20","gcCount":"28406612","gcPercent":43.5,"genbankAccession":"CM000682.2","length":64444167,"refseqAccession":"NC_000020.11","role":"assembled-molecule","ucscStyleName":"chr20"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"21","gcCount":"18981353","gcPercent":41.0,"genbankAccession":"CM000683.2","length":46709983,"refseqAccession":"NC_000021.9","role":"assembled-molecule","ucscStyleName":"chr21"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"22","gcCount":"20315771","gcPercent":47.0,"genbankAccession":"CM000684.2","length":50818468,"refseqAccession":"NC_000022.11","role":"assembled-molecule","ucscStyleName":"chr22","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"X","gcCount":"67807309","gcPercent":39.5,"genbankAccession":"CM000685.2","length":156040895,"refseqAccession":"NC_000023.11","role":"assembled-molecule","ucscStyleName":"chrX"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"Y","gcCount":"10963787","gcPercent":40.0,"genbankAccession":"CM000686.2","length":57227415,"refseqAccession":"NC_000024.10","role":"assembled-molecule","ucscStyleName":"chrY","unlocalizedCount":1}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270706.1","length":175055,"refseqAccession":"NT_187361.1","role":"unlocalized-scaffold","ucscStyleName":"chr1_KI270706v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270707.1","length":32032,"refseqAccession":"NT_187362.1","role":"unlocalized-scaffold","ucscStyleName":"chr1_KI270707v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270708.1","length":127682,"refseqAccession":"NT_187363.1","role":"unlocalized-scaffold","ucscStyleName":"chr1_KI270708v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270709.1","length":66860,"refseqAccession":"NT_187364.1","role":"unlocalized-scaffold","ucscStyleName":"chr1_KI270709v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270710.1","length":40176,"refseqAccession":"NT_187365.1","role":"unlocalized-scaffold","ucscStyleName":"chr1_KI270710v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270711.1","length":42210,"refseqAccession":"NT_187366.1","role":"unlocalized-scaffold","ucscStyleName":"chr1_KI270711v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270712.1","length":176043,"refseqAccession":"NT_187367.1","role":"unlocalized-scaffold","ucscStyleName":"chr1_KI270712v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270713.1","length":40745,"refseqAccession":"NT_187368.1","role":"unlocalized-scaffold","ucscStyleName":"chr1_KI270713v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270714.1","length":41717,"refseqAccession":"NT_187369.1","role":"unlocalized-scaffold","ucscStyleName":"chr1_KI270714v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"2","genbankAccession":"KI270715.1","length":161471,"refseqAccession":"NT_187370.1","role":"unlocalized-scaffold","ucscStyleName":"chr2_KI270715v1_random","unlocalizedCount":2}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"2","genbankAccession":"KI270716.1","length":153799,"refseqAccession":"NT_187371.1","role":"unlocalized-scaffold","ucscStyleName":"chr2_KI270716v1_random","unlocalizedCount":2}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"3","genbankAccession":"GL000221.1","length":155397,"refseqAccession":"NT_167215.1","role":"unlocalized-scaffold","ucscStyleName":"chr3_GL000221v1_random","unlocalizedCount":1}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"4","genbankAccession":"GL000008.2","length":209709,"refseqAccession":"NT_113793.3","role":"unlocalized-scaffold","ucscStyleName":"chr4_GL000008v2_random","unlocalizedCount":1}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"5","genbankAccession":"GL000208.1","length":92689,"refseqAccession":"NT_113948.1","role":"unlocalized-scaffold","ucscStyleName":"chr5_GL000208v1_random","unlocalizedCount":1}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"9","genbankAccession":"KI270717.1","length":40062,"refseqAccession":"NT_187372.1","role":"unlocalized-scaffold","ucscStyleName":"chr9_KI270717v1_random","unlocalizedCount":4}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"9","genbankAccession":"KI270718.1","length":38054,"refseqAccession":"NT_187373.1","role":"unlocalized-scaffold","ucscStyleName":"chr9_KI270718v1_random","unlocalizedCount":4}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"9","genbankAccession":"KI270719.1","length":176845,"refseqAccession":"NT_187374.1","role":"unlocalized-scaffold","ucscStyleName":"chr9_KI270719v1_random","unlocalizedCount":4}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"9","genbankAccession":"KI270720.1","length":39050,"refseqAccession":"NT_187375.1","role":"unlocalized-scaffold","ucscStyleName":"chr9_KI270720v1_random","unlocalizedCount":4}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"11","genbankAccession":"KI270721.1","length":100316,"refseqAccession":"NT_187376.1","role":"unlocalized-scaffold","ucscStyleName":"chr11_KI270721v1_random","unlocalizedCount":1}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"GL000009.2","length":201709,"refseqAccession":"NT_113796.3","role":"unlocalized-scaffold","ucscStyleName":"chr14_GL000009v2_random","unlocalizedCount":8}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"GL000194.1","length":191469,"refseqAccession":"NT_113888.1","role":"unlocalized-scaffold","ucscStyleName":"chr14_GL000194v1_random","unlocalizedCount":8}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"GL000225.1","length":211173,"refseqAccession":"NT_167219.1","role":"unlocalized-scaffold","ucscStyleName":"chr14_GL000225v1_random","unlocalizedCount":8}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"KI270722.1","length":194050,"refseqAccession":"NT_187377.1","role":"unlocalized-scaffold","ucscStyleName":"chr14_KI270722v1_random","unlocalizedCount":8}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"KI270723.1","length":38115,"refseqAccession":"NT_187378.1","role":"unlocalized-scaffold","ucscStyleName":"chr14_KI270723v1_random","unlocalizedCount":8}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"KI270724.1","length":39555,"refseqAccession":"NT_187379.1","role":"unlocalized-scaffold","ucscStyleName":"chr14_KI270724v1_random","unlocalizedCount":8}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"KI270725.1","length":172810,"refseqAccession":"NT_187380.1","role":"unlocalized-scaffold","ucscStyleName":"chr14_KI270725v1_random","unlocalizedCount":8}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"KI270726.1","length":43739,"refseqAccession":"NT_187381.1","role":"unlocalized-scaffold","ucscStyleName":"chr14_KI270726v1_random","unlocalizedCount":8}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"15","genbankAccession":"KI270727.1","length":448248,"refseqAccession":"NT_187382.1","role":"unlocalized-scaffold","ucscStyleName":"chr15_KI270727v1_random","unlocalizedCount":1}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"16","genbankAccession":"KI270728.1","length":1872759,"refseqAccession":"NT_187383.1","role":"unlocalized-scaffold","ucscStyleName":"chr16_KI270728v1_random","unlocalizedCount":1}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"17","genbankAccession":"GL000205.2","length":185591,"refseqAccession":"NT_113930.2","role":"unlocalized-scaffold","ucscStyleName":"chr17_GL000205v2_random","unlocalizedCount":3}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"17","genbankAccession":"KI270729.1","length":280839,"refseqAccession":"NT_187384.1","role":"unlocalized-scaffold","ucscStyleName":"chr17_KI270729v1_random","unlocalizedCount":3}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"17","genbankAccession":"KI270730.1","length":112551,"refseqAccession":"NT_187385.1","role":"unlocalized-scaffold","ucscStyleName":"chr17_KI270730v1_random","unlocalizedCount":3}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"22","genbankAccession":"KI270731.1","length":150754,"refseqAccession":"NT_187386.1","role":"unlocalized-scaffold","ucscStyleName":"chr22_KI270731v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"22","genbankAccession":"KI270732.1","length":41543,"refseqAccession":"NT_187387.1","role":"unlocalized-scaffold","ucscStyleName":"chr22_KI270732v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"22","genbankAccession":"KI270733.1","length":179772,"refseqAccession":"NT_187388.1","role":"unlocalized-scaffold","ucscStyleName":"chr22_KI270733v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"22","genbankAccession":"KI270734.1","length":165050,"refseqAccession":"NT_187389.1","role":"unlocalized-scaffold","ucscStyleName":"chr22_KI270734v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"22","genbankAccession":"KI270735.1","length":42811,"refseqAccession":"NT_187390.1","role":"unlocalized-scaffold","ucscStyleName":"chr22_KI270735v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"22","genbankAccession":"KI270736.1","length":181920,"refseqAccession":"NT_187391.1","role":"unlocalized-scaffold","ucscStyleName":"chr22_KI270736v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"22","genbankAccession":"KI270737.1","length":103838,"refseqAccession":"NT_187392.1","role":"unlocalized-scaffold","ucscStyleName":"chr22_KI270737v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"22","genbankAccession":"KI270738.1","length":99375,"refseqAccession":"NT_187393.1","role":"unlocalized-scaffold","ucscStyleName":"chr22_KI270738v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"22","genbankAccession":"KI270739.1","length":73985,"refseqAccession":"NT_187394.1","role":"unlocalized-scaffold","ucscStyleName":"chr22_KI270739v1_random","unlocalizedCount":9}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"Y","genbankAccession":"KI270740.1","length":37240,"refseqAccession":"NT_187395.1","role":"unlocalized-scaffold","ucscStyleName":"chrY_KI270740v1_random","unlocalizedCount":1}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"GL000195.1","length":182896,"refseqAccession":"NT_113901.1","role":"unplaced-scaffold","ucscStyleName":"chrUn_GL000195v1"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"GL000213.1","length":164239,"refseqAccession":"NT_167208.1","role":"unplaced-scaffold","ucscStyleName":"chrUn_GL000213v1"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"GL000214.1","length":137718,"refseqAccession":"NT_167209.1","role":"unplaced-scaffold","ucscStyleName":"chrUn_GL000214v1"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"GL000216.2","length":176608,"refseqAccession":"NT_167211.2","role":"unplaced-scaffold","ucscStyleName":"chrUn_GL000216v2"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"GL000218.1","length":161147,"refseqAccession":"NT_113889.1","role":"unplaced-scaffold","ucscStyleName":"chrUn_GL000218v1"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"GL000219.1","length":179198,"refseqAccession":"NT_167213.1","role":"unplaced-scaffold","ucscStyleName":"chrUn_GL000219v1"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"GL000220.1","length":161802,"refseqAccession":"NT_167214.1","role":"unplaced-scaffold","ucscStyleName":"chrUn_GL000220v1"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"GL000224.1","length":179693,"refseqAccession":"NT_167218.1","role":"unplaced-scaffold","ucscStyleName":"chrUn_GL000224v1"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"GL000226.1","length":15008,"refseqAccession":"NT_167220.1","role":"unplaced-scaffold","ucscStyleName":"chrUn_GL000226v1"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270302.1","length":2274,"refseqAccession":"NT_187396.1","role":"unplaced-scaffold","ucscStyleName":"chrUn_KI270302v1"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270303.1","length":1942,"refseqAccession":"NT_187398.1","role":"unplaced-scaffold","ucscStyleName":"chrUn_KI270303v1"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"Primary Assembly","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270304.1","length":2165,"refseqAccession":"NT_187397.1","role":"unplaced-scaffold","ucscStyleName":"chrUn_KI270304v1"}
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{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"ALT_REF_LOCI_18","assignedMoleculeLocationType":"Chromosome","chrName":"19","genbankAccession":"KI270890.1","length":184499,"refseqAccession":"NT_187644.1","role":"alt-scaffold","ucscStyleName":"chr19_KI270890v1_alt"}
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{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"ALT_REF_LOCI_22","assignedMoleculeLocationType":"Chromosome","chrName":"19","genbankAccession":"KI270916.1","length":184516,"refseqAccession":"NT_187670.1","role":"alt-scaffold","ucscStyleName":"chr19_KI270916v1_alt"}
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{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"ALT_REF_LOCI_35","assignedMoleculeLocationType":"Chromosome","chrName":"19","genbankAccession":"GL000209.2","length":177381,"refseqAccession":"NT_113949.2","role":"alt-scaffold","ucscStyleName":"chr19_GL000209v2_alt"}
{"assemblyAccession":"GCF_000001405.26","assemblyUnit":"non-nuclear","assignedMoleculeLocationType":"Mitochondrion","chrName":"MT","gcCount":"7350","gcPercent":44.0,"genbankAccession":"J01415.2","length":16569,"refseqAccession":"NC_012920.1","role":"assembled-molecule","ucscStyleName":"chrM"} |
Perhaps a short term solution is to transform the above into the current required input format, that way we don't have to update the tool. |
I was able to generate a file similar to
# After extracting only data under reports and converting to jsonl, the output can also be used by dataformat.
jq -c '.reports[]' sequence_report.curl.json > sequence_report.curl_jq_reports_as_jsonl.jsonl
.
# Convert JSONL to TSV.
./dataformat tsv genome-seq --inputfile sequence_report.curl_jq_reports_as_jsonl.jsonl > sequence_report.curl_jq_reports_as_jsonl.tsv
# Convert JSONL to TSV, but only for certain columns:
./dataformat tsv genome-seq --inputfile sequence_report.curl_jq_reports_as_jsonl.jsonl --fields chr-name,role,mol-type,genbank-seq-acc,refseq-seq-acc,assm-unit-acc,seq-length,ucsc-style-name > sequence_report.curl_jq_reports_as_jsonl.dataformat_fields.tsv They generated the same output although the keys in the JSONL have different casings:
Full TSV file and filtered on certain fields:
Old
It would be nice that |
Support NCBI sequence_report.jsonl as input for CollectAlternateContigNames, as it seems that NCBI now prefers that format,
instead of the old https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.26_GRCh38/GCF_000001405.26_GRCh38_assembly_report.txt
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