{"__v":0,"_id":"57989ac917ced017003c4c6a","category":{"__v":0,"_id":"57989a8817ced017003c4c69","project":"57618347b65324200072d6a5","version":"57618347b65324200072d6a8","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-07-27T11:27:04.750Z","from_sync":false,"order":3,"slug":"docstrings","title":"Documentation"},"parentDoc":null,"project":"57618347b65324200072d6a5","user":"57617c8caa540f3600bfed20","version":{"__v":8,"_id":"57618347b65324200072d6a8","project":"57618347b65324200072d6a5","createdAt":"2016-06-15T16:33:11.587Z","releaseDate":"2016-06-15T16:33:11.587Z","categories":["57618347b65324200072d6a9","5761912d207db7170022fbe9","57619455a7c9f729009a74e0","576e8ae1f37ab41700147471","5797b8e5209a6e0e00b8321b","57989a8817ced017003c4c69","579ca6f3d46f960e0029a8ec","579ca703fefb1d0e00c94f06"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":true,"codename":"blobtools v0.9.19","version_clean":"0.9.19","version":"0.9.19"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-07-27T11:28:09.480Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":0,"body":"[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"usage: blobtools create     -i FASTA [-y FASTATYPE] [-o PREFIX] [--title TITLE]\\n                              [-b BAM...] [-s SAM...] [-a CAS...] [-c COV...]\\n                              [--nodes <NODES>] [--names <NAMES>] [--db <NODESDB>]\\n                              [-t HITS...] [-x TAXRULE...] [-m INT] [--tax_collision_random]\\n                              [-h|--help]\\n\\n    Options:\\n        -h --help                       show this\\n        -i, --infile FASTA              FASTA file of assembly. Headers are split at whitespaces.\\n        -y, --type FASTATYPE            Assembly program used to create FASTA. If specified,\\n                                        coverage will be parsed from FASTA header.\\n                                        (Parsing supported for 'spades', \\n                                        'soap', 'velvet', 'abyss', 'platanus')\\n        -t, --hitsfile HITS...          Hits file in format (qseqid\\\\ttaxid\\\\tbitscore)\\n                                        (e.g. BLAST output \\\"--outfmt '6 qseqid staxids bitscore'\\\")\\n        -x, --taxrule <TAXRULE>...      Taxrule determines how taxonomy \\n        \\t\\t\\t\\t\\t\\t\\t\\t\\t\\t\\t\\t\\t\\t\\t\\tof blobs is computed [default: bestsum]\\n                                        \\\"bestsum\\\"       : sum bitscore across all \\n                                        hits for each taxonomic rank\\n                                        \\\"bestsumorder\\\"  : sum bitscore across all \\n                                        hits for each taxonomic rank.\\n                                                  - If first <TAX> file supplies \\n                                                  hits, bestsum is calculated.\\n                                                  - If no hit is found, the \\n                                                  next <TAX> file is used.\\n        -m, --min_diff <FLOAT>          Minimal score difference between highest scoring\\n                                        taxonomies (otherwise \\\"unresolved\\\") [default: 0.0]\\n        --tax_collision_random          Random allocation of taxonomy if highest scoring\\n                                        taxonomies have equal scores (otherwise \\\"unresolved\\\")\\n        --nodes <NODES>                 NCBI nodes.dmp file. Not required if '--db'\\n        --names <NAMES>                 NCBI names.dmp file. Not required if '--db'\\n        --db <NODESDB>                  NodesDB file (default: $BLOBTOOLS/data/nodesDB.txt).\\n        -b, --bam <BAM>...              BAM file(s) (requires samtools in $PATH)\\n        -s, --sam <SAM>...              SAM file(s)\\n        -a, --cas <CAS>...              CAS file(s) (requires clc_mapping_info in $PATH)\\n        -c, --cov <COV>...              TAB separated. (seqID\\\\tcoverage)\\n        -o, --out <PREFIX>              BlobDB output prefix\\n        --title TITLE                   Title of BlobDB [default: output prefix)\\n\",\n      \"language\": \"text\"\n    }\n  ]\n}\n[/block]","excerpt":"","slug":"create","type":"basic","title":"create"}
[block:code] { "codes": [ { "code": "usage: blobtools create -i FASTA [-y FASTATYPE] [-o PREFIX] [--title TITLE]\n [-b BAM...] [-s SAM...] [-a CAS...] [-c COV...]\n [--nodes <NODES>] [--names <NAMES>] [--db <NODESDB>]\n [-t HITS...] [-x TAXRULE...] [-m INT] [--tax_collision_random]\n [-h|--help]\n\n Options:\n -h --help show this\n -i, --infile FASTA FASTA file of assembly. Headers are split at whitespaces.\n -y, --type FASTATYPE Assembly program used to create FASTA. If specified,\n coverage will be parsed from FASTA header.\n (Parsing supported for 'spades', \n 'soap', 'velvet', 'abyss', 'platanus')\n -t, --hitsfile HITS... Hits file in format (qseqid\\ttaxid\\tbitscore)\n (e.g. BLAST output \"--outfmt '6 qseqid staxids bitscore'\")\n -x, --taxrule <TAXRULE>... Taxrule determines how taxonomy \n \t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tof blobs is computed [default: bestsum]\n \"bestsum\" : sum bitscore across all \n hits for each taxonomic rank\n \"bestsumorder\" : sum bitscore across all \n hits for each taxonomic rank.\n - If first <TAX> file supplies \n hits, bestsum is calculated.\n - If no hit is found, the \n next <TAX> file is used.\n -m, --min_diff <FLOAT> Minimal score difference between highest scoring\n taxonomies (otherwise \"unresolved\") [default: 0.0]\n --tax_collision_random Random allocation of taxonomy if highest scoring\n taxonomies have equal scores (otherwise \"unresolved\")\n --nodes <NODES> NCBI nodes.dmp file. Not required if '--db'\n --names <NAMES> NCBI names.dmp file. Not required if '--db'\n --db <NODESDB> NodesDB file (default: $BLOBTOOLS/data/nodesDB.txt).\n -b, --bam <BAM>... BAM file(s) (requires samtools in $PATH)\n -s, --sam <SAM>... SAM file(s)\n -a, --cas <CAS>... CAS file(s) (requires clc_mapping_info in $PATH)\n -c, --cov <COV>... TAB separated. (seqID\\tcoverage)\n -o, --out <PREFIX> BlobDB output prefix\n --title TITLE Title of BlobDB [default: output prefix)\n", "language": "text" } ] } [/block]