bh20-seq-resource/scripts/download_genbank_data, branch fasta-subset-from-query Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis http://git.systemreboot.net/bh20-seq-resource/atom?h=fasta-subset-from-query 2020-09-28T09:57:51+00:00 new countries; updated genbank/sra scripts to manage more specimen sources 2020-09-28T09:57:51+00:00 AndreaGuarracino 2020-09-28T09:57:51+00:00 urn:sha1:c72dab2788d010153d5406f2d5ecbe3824571931 genbank and sra scripts more picky on the ontologies; added utils.py for shared functions 2020-09-28T07:13:50+00:00 AndreaGuarracino 2020-09-28T07:13:50+00:00 urn:sha1:bc2e51bc8418876cc826482ece10874b2a61fa03 added in the sra script an option to include only a subset of ids 2020-09-04T09:13:25+00:00 AndreaGuarracino 2020-09-04T09:13:25+00:00 urn:sha1:327b6db4e7c9ceda190617f2a793e6a646bb30cc synchronized the create_sra_metadata.py script with the latest updates 2020-09-04T07:59:47+00:00 AndreaGuarracino 2020-09-04T07:59:47+00:00 urn:sha1:842f1a25cc2632771e8a816dbb4898db81d7a6c2 added control (locally and in the validation) that sample_id has to be the same in the metadata and in the FASTA header #103 2020-08-28T09:16:24+00:00 AndreaGuarracino 2020-08-28T09:16:24+00:00 urn:sha1:3165a31e321cbf4641f9afdcbea511ee66f673bb updated dependency from clustalw to minimap2; the genbank script no longer creates YAML/FASTA pairs for too short sequences 2020-08-26T22:18:24+00:00 AndreaGuarracino 2020-08-26T22:18:24+00:00 urn:sha1:4299c750728bbad4bdbf0311ff2a4b9c65d9883c added option in the genbank script to ignore (already validated) IDs; code cleaning; typos 2020-08-26T14:56:47+00:00 AndreaGuarracino 2020-08-26T14:56:47+00:00 urn:sha1:9107e59b2e69c4f3f3369175d57631ed878009e7 the YAML/FASTA pair is not created for samples where at least one mandatory field is missing 2020-08-24T22:02:32+00:00 AndreaGuarracino 2020-08-24T22:02:32+00:00 urn:sha1:2baa88b766ec540bd34b96599014dd16e393af39 genbank/sra scripts update to be more generic with the specimen sources 2020-08-23T09:28:02+00:00 AndreaGuarracino 2020-08-23T09:28:02+00:00 urn:sha1:3b9423891c4e90499a40c1be029ef40160efb557 genbank/sra scripts updated to read the dictionaries in a more general way 2020-08-22T14:41:02+00:00 AndreaGuarracino 2020-08-22T14:41:02+00:00 urn:sha1:d6559a65865ebbb14e041893c2dae742fa146143