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| 1 | +# blobtools |
| 2 | +Application for the visualisation of draft genome assemblies and general QC |
| 3 | + |
| 4 | +- Requirements |
| 5 | + |
| 6 | +``` |
| 7 | +pip install matplotlib |
| 8 | +pip install docopt |
| 9 | +``` |
| 10 | + |
| 11 | +- blobtools : main executable |
| 12 | +``` |
| 13 | +usage: blobtools <command> [<args>...] [--help] |
| 14 | +
|
| 15 | +commands: |
| 16 | + create create a BlobDB |
| 17 | + view print BlobDB |
| 18 | + plot plot BlobDB as a blobplot |
| 19 | +
|
| 20 | +-h --help show this |
| 21 | +``` |
| 22 | + |
| 23 | +- blobtools create : create a BlobDb JSON file |
| 24 | +``` |
| 25 | +usage: blobtools create -i FASTA [-y FASTATYPE] [-o OUTFILE] [--title TITLE] |
| 26 | + [-b BAM...] [-s SAM...] [-a CAS...] [-c COV...] |
| 27 | + [--nodes <NODES>] [--names <NAMES>] [--db <NODESDB>] |
| 28 | + [-t TAX...] [-r TAXRULE...] |
| 29 | + [-h|--help] |
| 30 | + |
| 31 | + Options: |
| 32 | + -h --help show this |
| 33 | + -i, --infile FASTA FASTA file of assembly. Headers are split at whitespaces. |
| 34 | + -y, --type FASTATYPE Assembly program used to create FASTA. If specified, |
| 35 | + coverage will be parsed from FASTA header. |
| 36 | + (Parsing supported for 'spades', 'soap', 'velvet', 'abyss') |
| 37 | + -t, --taxfile TAX... Taxonomy file in format (qseqid\ttaxid\tbitscore) |
| 38 | + (e.g. BLAST output "--outfmt '6 qseqid staxids bitscore'") |
| 39 | + -r, --taxrule <TAXRULE>... Taxrule determines how taxonomy of blobs is computed [default: bestsum] |
| 40 | + "bestsum" : sum bitscore across all hits for each taxonomic rank |
| 41 | + "bestsumorder" : sum bitscore across all hits for each taxonomic rank. |
| 42 | + - If first <TAX> file supplies hits, bestsum is calculated. |
| 43 | + - If no hit is found, the next <TAX> file is used. |
| 44 | + --nodes <NODES> NCBI nodes.dmp file. Not required if '--db' |
| 45 | + --names <NAMES> NCBI names.dmp file. Not required if '--db' |
| 46 | + --db <NODESDB> NodesDB file [default: data/nodesDB.txt]. |
| 47 | + -b, --bam <BAM>... BAM file (requires samtools in $PATH) |
| 48 | + -s, --sam <SAM>... SAM file |
| 49 | + -a, --cas <CAS>... CAS file (requires clc_mapping_info in $PATH) |
| 50 | + -c, --cov <COV>... TAB separated. (seqID\tcoverage) |
| 51 | + -o, --out <OUT> BlobDB output prefix |
| 52 | + --title TITLE Title of BlobDB [default: FASTA) |
| 53 | +``` |
| 54 | + |
| 55 | +- blobtools view : generate table output from a blobDB file |
| 56 | +``` |
| 57 | +usage: blobtools view -i <BLOBDB> [-r <TAXRULE>] [--rank <TAXRANK>...] [--hits] |
| 58 | + [--list <LIST>] [--out <OUT>] |
| 59 | + [--h|--help] |
| 60 | + |
| 61 | + Options: |
| 62 | + --h --help show this |
| 63 | + -i, --input <BLOBDB> BlobDB file (created with "blobtools forge") |
| 64 | + -o, --out <OUT> Output file [default: STDOUT] |
| 65 | + -l, --list <LIST> List of sequence names (comma-separated or file). |
| 66 | + If comma-separated, no whitespaces allowed. |
| 67 | + -r, --taxrule <TAXRULE> Taxrule used for computing taxonomy (supported: "bestsum", "bestsumorder") |
| 68 | + [default: bestsum] |
| 69 | + --rank <TAXRANK>... Taxonomic rank(s) at which output will be written. |
| 70 | + (supported: 'species', 'genus', 'family', 'order', |
| 71 | + 'phylum', 'superkingdom', 'all') [default: phylum] |
| 72 | + -b, --hits Displays taxonomic hits from tax files |
| 73 | +``` |
| 74 | + |
| 75 | +blobtools plot : generate a blobplot from a blobDB file |
| 76 | +``` |
| 77 | +usage: blobtools plot -i BLOBDB [-p INT] [-l INT] [-c] [-n] [-s] |
| 78 | + [-r RANK] [-x TAXRULE] [--label GROUPS...] |
| 79 | + [-o PREFIX] [-m] [--sort ORDER] [--hist HIST] [--title] |
| 80 | + [--colours FILE] [--include FILE] [--exclude FILE] |
| 81 | + [--format FORMAT] [--noblobs] [--noreads] [--refcov FILE] |
| 82 | + [-h|--help] |
| 83 | +
|
| 84 | + Options: |
| 85 | + -h --help show this |
| 86 | + -i, --infile BLOBDB BlobDB file |
| 87 | + -p, --plotgroups INT Number of (taxonomic) groups to plot, remaining |
| 88 | + groups are placed in 'other' [default: 7] |
| 89 | + -l, --length INT Minimum sequence length considered for plotting [default: 100] |
| 90 | + -c, --cindex Colour blobs by 'c index' [default: False] |
| 91 | + -n, --nohit Hide sequences without taxonomic annotation [default: False] |
| 92 | + -s, --noscale Do not scale sequences by length [default: False] |
| 93 | + -o, --out PREFIX Output prefix |
| 94 | + -m, --multiplot Multi-plot. Print plot after addition of each (taxonomic) group |
| 95 | + [default: False] |
| 96 | + --sort <ORDER> Sort order for plotting [default: span] |
| 97 | + span : plot with decreasing span |
| 98 | + count : plot with decreasing count |
| 99 | + --hist <HIST> Data for histograms [default: span] |
| 100 | + span : span-weighted histograms |
| 101 | + count : count histograms |
| 102 | + --title Add title of BlobDB to plot [default: False] |
| 103 | + -r, --rank RANK Taxonomic rank used for colouring of blobs [default: phylum] |
| 104 | + (Supported: species, genus, family, order, phylum, superkingdom) |
| 105 | + -x, --taxrule TAXRULE Taxrule which has been used for computing taxonomy |
| 106 | + (Supported: bestsum, bestsumorder) [default: bestsum] |
| 107 | + --label GROUPS... Relabel (taxonomic) groups (not 'all' or 'other'), |
| 108 | + e.g. "Bacteria=Actinobacteria,Proteobacteria" |
| 109 | + --colours COLOURFILE File containing colours for (taxonomic) groups |
| 110 | + --exclude GROUPS.. Place these (taxonomic) groups in 'other', |
| 111 | + e.g. "Actinobacteria,Proteobacteria" |
| 112 | + --format FORMAT Figure format for plot (png, pdf, eps, jpeg, |
| 113 | + ps, svg, svgz, tiff) [default: png] |
| 114 | + --noblobs Omit blobplot [default: False] |
| 115 | + --noreads Omit plot of reads mapping [default: False] |
| 116 | + --refcov FILE File containing number of "total" and "mapped" reads |
| 117 | + per coverage file. (e.g.: bam0,900,100). If provided, info |
| 118 | + will be used in read coverage plot(s). |
| 119 | +``` |
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