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CLI Reference
Linxira Wiki edited this page Aug 15, 2026
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linxira-bio 是人和工作流共用的命令行界面。所有分析类命令支持 --json 输出结构化信封。按域分组,完整清单:
linxira-bio capabilities [--json]
linxira-bio doctor [--json]
linxira-bio environment audit [--json]
linxira-bio environment plan [PROFILE] [--mode MODE] [--project-root PATH] [--json]
linxira-bio environment apply [PROFILE] [--mode MODE] [--project-root PATH] [--json]
linxira-bio runtime catalog [--json]
linxira-bio workflow packs [--json]
linxira-bio workflow run <pack-id> <request.json> <result.json>
linxira-bio dataset inspect <input> [--json]
linxira-bio table manipulate <input.csv|tsv[.gz]> <output.csv|tsv> [--select-column NAME ...] [--drop-column NAME ...] [--filter-column NAME --filter-op equals|contains|non-empty [--filter-value VALUE]] [--skip-rows N] [--limit N] [--delimiter csv|tsv] [--output-delimiter csv|tsv] [--json]
linxira-bio export table <input.json> <output.csv|tsv|json|jsonl|xlsx> [--json]
linxira-bio sequence stats <input.fasta[.gz]> [--json]
linxira-bio sequence extract <input.fasta[.gz]> <output.fasta> [--id ID ...] [--region ID:START-END[:+|-] ...] [--strict] [--json]
linxira-bio sequence filter <input.fasta[.gz]> <output.fasta> [--min-length N] [--max-length N] [--min-gc-percent P] [--max-gc-percent P] [--max-n-percent P] [--json]
linxira-bio sequence reverse-complement <input.fasta[.gz]> <output.fasta> [--json]
linxira-bio sequence translate <input.fasta[.gz]> <output.fasta> [--frame FRAME ...] [--trim-terminal-stop] [--stop-at-first] [--json]
linxira-bio sequence orf <input.fasta[.gz]> <output.fasta> [--min-amino-acids N] [--forward-only] [--include-partial-3prime] [--json]
linxira-bio sequence normalize-ids <input.fasta[.gz]> <output.fasta> [--prefix PREFIX] [--start N] [--width N|--no-padding] [--drop-description] [--json]
linxira-bio sequence merge <output.fasta> <input.fasta[.gz]>... [--allow-duplicate-ids] [--json]
linxira-bio sequence split <input.fasta[.gz]> <output-dir> [--records-per-file N] [--prefix PREFIX] [--json]
linxira-bio sequence to-table <input.fasta[.gz]> <output.csv|tsv> [--delimiter csv|tsv] [--no-header] [--json]
linxira-bio sequence from-table <input.csv|tsv[.gz]> <output.fasta> [--delimiter csv|tsv] [--id-column NAME] [--sequence-column NAME] [--description-column NAME|--no-description-column] [--json]
linxira-bio sequence kmer-count <input.fasta[.gz]> <output.tsv> [--k N] [--canonical] [--top-n N] [--json]
linxira-bio sequence consensus <input.alignment.fasta> <output.fasta> [--threshold FLOAT] [--json]
linxira-bio sequence shuffle <input.fasta[.gz]> <output.fasta> [--seed N] [--json]
linxira-bio sequence convert <input> <output> [--input-format fasta|fastq|genbank|embl] [--output-format fasta|fastq|genbank|embl]
linxira-bio chemistry descriptors <input.sdf> <output.tsv> [--json]
linxira-bio medical survival <cohort.csv|tsv> <output-directory> --time-column COLUMN --event-column COLUMN --group-column COLUMN --reference-level LEVEL [--json]
linxira-bio medical cohort-qc <cohort.csv|tsv[.gz]> [--json]
linxira-bio medical single-cell-qc <counts.csv|tsv[.gz]> [--json]
linxira-bio medical pathway <genes.txt|csv|tsv> <associations.csv|tsv> [--min-overlap N] [--max-terms N] [--include-genes] [--json]
linxira-bio medical variant-cohort <cohort.vcf[.gz]> [--json]
linxira-bio medical pharmacogenomics <input.vcf[.gz]> <output.tsv> [--json]
linxira-bio medical spatial-transcriptomics <matrix.mtx[.gz]> <features.tsv[.gz]> <barcodes.tsv[.gz]> <output.tsv> [--json]
linxira-bio medical microbiome <reads.fa|fq> <output.tsv> --database <kraken2-db> [--confidence FRACTION] [--minimum-hit-groups N] [--threads N] [--json]
linxira-bio medical metabolomics <input.mzML[.gz]> <output.tsv> [--json]
linxira-bio primer epcr <reference.fasta[.gz]> <primers.tsv> <output.tsv> [--min-amplicon N] [--max-amplicon N] [--max-hits N] [--json]
linxira-bio fastq qc <input.fastq[.gz]> [--quality-encoding MODE] [--max-cycles N] [--json]
linxira-bio fastq trim <input.fastq[.gz]> <output.fastq> [--min-quality N] [--min-length N] [--quality-encoding phred+33|phred+64] [--json]
linxira-bio fastq adapter-trim <input.fastq[.gz]> <output.fastq> [--adapter SEQ ...] [--min-overlap N] [--min-length N] [--json]
linxira-bio fastq deduplicate <input.fastq[.gz]> <output.fastq> [--header-umi-delimiter TEXT | --sequence-prefix-umi N] [--json]
linxira-bio fastq subsample <input.fastq[.gz]> <output.fastq> [--target-count N | --fraction F] [--seed N] [--json]
linxira-bio alignment qc <input.sam[.gz]> [--json]
linxira-bio alignment bam-cram-qc <input.bam|cram> <output.tsv> [--reference reference.fasta] [--json]
linxira-bio alignment coverage <input.bam|cram> <output.tsv> [--reference reference.fasta] [--json]
linxira-bio alignment bam-to-bigwig <input.bam|cram> <output.bw> [--threads N] [--json]
linxira-bio alignment short-read <reference.fasta> <reads.fastq> <output.bam> [--threads N] [--json]
linxira-bio alignment long-read <reference.fasta> <reads.fastq> <output.sam> [--preset map-ont|map-pb|map-hifi|splice] [--threads N] [--secondary] [--json]
linxira-bio annotation stats <input.gff3|gtf[.gz]> [--json]
linxira-bio annotation normalize <input.gff3|gtf[.gz]> <output.gff3> [--sort] [--json]
linxira-bio annotation positions <input.gff3|gtf[.gz]> <output.tsv> [--feature-type TYPE ...] [--json]
linxira-bio annotation extract <input.gff3|gtf[.gz]> <reference.fasta[.gz]> <output.fasta> [--feature-type gene|transcript|cds|exon|utr|five_prime_utr|three_prime_utr|promoter] [--promoter-length N] [--json]
linxira-bio annotation gene-density <input.gff3|gtf[.gz]> [--feature-type TYPE ...] [--window-size N] [--step-size N] [--json]
linxira-bio annotation go <input.csv|tsv[.gz]> <output.tsv> [--gene-column NAME] [--go-column NAME] [--json]
linxira-bio annotation eggnog <input.tsv[.gz]> <output.tsv> [--json]
linxira-bio annotation plot <input.gff3|gtf[.gz]> <output.svg> [--feature-id ID | --seqid NAME] [--max-features N] [--json]
linxira-bio variant stats <input.vcf[.gz]> [--json]
linxira-bio variant compare <left.vcf[.gz]> <right.vcf[.gz]> [--json]
linxira-bio variant filter <input.vcf[.gz]> <output.vcf> [--min-qual Q] [--pass-only] [--contig NAME ...] [--min-info-dp N] [--json]
linxira-bio variant normalize <input.vcf[.gz]> <reference.fasta[.gz]> <output.vcf> [--json]
linxira-bio variant to-table <input.vcf[.gz]> <output.tsv> [--json]
linxira-bio variant annotate <input.vcf> <output.vcf> [--database DB] [--upstream-downstream N] [--no-stats] [--json]
linxira-bio interval intersect <left.bed[.gz]> <right.bed[.gz]> [--json]
linxira-bio interval merge <input.bed[.gz]> <output.bed> [--max-gap N] [--json]
linxira-bio interval subtract <left.bed[.gz]> <right.bed[.gz]> <output.bed> [--json]
linxira-bio interval closest <query.bed[.gz]> <target.bed[.gz]> <output.tsv> [--json]
linxira-bio expression matrix-qc <matrix.csv|tsv[.gz]> [--json]
linxira-bio expression normalize <matrix.csv|tsv[.gz]> <output.tsv> [--method cpm|log2-cpm|median-ratio] [--pseudocount X] [--json]
linxira-bio expression pca <matrix.csv|tsv[.gz]> [--components N] [--scale] [--json]
linxira-bio expression cluster <matrix.csv|tsv[.gz]> [--sample-clusters N] [--feature-clusters N] [--max-iterations N] [--no-scale] [--json]
linxira-bio expression heatmap <matrix.csv|tsv[.gz]> [--top-features N] [--no-scale] [--json]
linxira-bio expression volcano <differential.csv> <output.svg> [--padj P] [--log2-fold-change X] [--max-points N] [--json]
linxira-bio expression wgcna <expression.csv|tsv> <output.json> [--min-expression X] [--min-samples N] [--min-module-size N] [--merge-cut-height X] [--network-type signed|unsigned|signed hybrid] [--power N] [--no-log-transform] [--threads N] [--json]
linxira-bio set venn <sets.csv|tsv[.gz]> [--include-items] [--json]
linxira-bio set upset <sets.csv|tsv[.gz]> [--max-intersections N] [--include-items] [--json]
linxira-bio enrichment custom <genes.txt|csv|tsv> <associations.csv|tsv[.gz]> [--min-overlap N] [--max-terms N] [--include-genes] [--json]
linxira-bio enrichment go <genes.txt|csv|tsv> <associations.csv|tsv[.gz]> [--min-overlap N] [--max-terms N] [--include-genes] [--json]
linxira-bio enrichment kegg <genes.txt|csv|tsv> <associations.csv|tsv[.gz]> [--min-overlap N] [--max-terms N] [--include-genes] [--json]
linxira-bio enrichment gsea <ranked-genes.csv|tsv> <gene-sets.csv|tsv> [--score-exponent X] [--min-set-size N] [--max-set-size N] [--permutations N] [--seed N] [--json]
linxira-bio enrichment visualize <genes.txt|csv|tsv> <associations.csv|tsv[.gz]> <output.svg> --kind custom|go|kegg [--style bar|dot|network] [--min-overlap N] [--max-terms N] [--json]
linxira-bio similarity blast-parse <blast.tsv|xml[.gz]> [--json]
linxira-bio similarity blast <query.fasta> <reference.fasta> <output.tsv> [--program blastn|blastp|blastx|tblastn|tblastx] [--threads N] [--evalue X] [--max-targets N] [--outfmt 6|7] [--json]
linxira-bio similarity diamond <query.fasta> <reference.fasta> <output.tsv> [--mode blastp|blastx] [--threads N] [--evalue X] [--max-targets N] [--outfmt 6|7] [--json]
linxira-bio similarity hmmer <profile.hmm> <sequences.fasta> <output.domtblout> [--mode hmmsearch|hmmscan] [--threads N] [--evalue X] [--json]
linxira-bio similarity rbh <forward.tsv|xml[.gz]> <reverse.tsv|xml[.gz]> [--max-evalue X] [--min-identity P] [--json]
linxira-bio motif meme <input.fasta> <output.meme> [--alphabet dna|rna|protein] [--distribution oops|zoops|anr] [--motifs N] [--min-width N] [--max-width N] [--threads N] [--json]
linxira-bio motif logo <input.meme> <output.svg> [--json]
linxira-bio motif mast <motif.meme> <sequences.fasta> <output.txt> [--evalue X] [--hit-list] [--threads N] [--json]
linxira-bio comparative synteny-plot <anchors.tsv> <output.svg> [--json]
linxira-bio protein properties <proteins.fasta[.gz]> [--json]
linxira-bio protein domains <interproscan.tsv|hmmer.domtblout[.gz]> [--json]
linxira-bio protein domain-plot <interproscan.tsv|hmmer.domtblout[.gz]> <output.svg> [--sequence-id ID] [--max-sequences N] [--max-domains N] [--json]
linxira-bio protein secondary-structure <structure.pdb|cif> <output.dssp> [--json]
linxira-bio structure pdb <input.pdb[.gz]> [--alphafold-plddt] [--json]
linxira-bio structure mmcif-summary <input.cif|mmcif[.gz]> [--json]
linxira-bio structure sequence <input.pdb|cif[.gz]> [--json]
linxira-bio structure contact-map <input.pdb|cif[.gz]> [--cutoff ANGSTROM] [--atom NAME] [--intra-chain-only] [--json]
linxira-bio structure geometry <input.pdb|cif[.gz]> --atom CHAIN/RESIDUE/ATOM --atom ... [--json]
linxira-bio structure superpose <reference.pdb|cif[.gz]> <mobile.pdb|cif[.gz]> [--atom NAME] [--json]
linxira-bio phylogeny tree <input.nwk[.gz]> <output.nwk> [--reroot LEAF] [--label-map labels.tsv] [--json]
linxira-bio phylogeny distance <input.alignment.fasta> <output.tsv> [--model p-distance|jc69|k80] [--json]
linxira-bio phylogeny iqtree <alignment> <output.newick> [--threads N] [--model MODEL] [--seed N] [--json]
linxira-bio msa muscle <input.fasta> <output.fasta> [--mode align|super5] [--threads N] [--json]
linxira-bio msa trimal <input.alignment> <output.alignment> [--mode automated1|gappyout|strict|strictplus|nogaps] [--json]
linxira-bio metagenomics classify <reads.fa|fq> <output.tsv> --database <kraken2-db> [--confidence FRACTION] [--minimum-hit-groups N] [--threads N] [--json]
linxira-bio rna secondary-structure <input.fa> <output.txt> [--temp C] [--json]
若干能力经
workflow run调用工作流包,见 Workflow-Packs;environment apply与protein.af2/af3相关命令保持规划,不可执行。