Package: variant
Python pakcage for genomic variant analysisHow to install?pip install variantHow to use?🧬variant motifsubcommand can fetch motif sequence around given site.Usage: variant motif [OPTIONS]

 Fetch genomic motif.

╭─ Options ─────────────────────────────────────────────────────────────────╮
│    --input        -i  TEXT  Input position file.                          │
│    --output       -o  TEXT  Output annotation file.                       │
│ *  --fasta        -f  TEXT  reference fasta file. [required]              │
│    --npad         -n  TEXT  Number of padding base to call motif. If you  │
│                             want to set different left and right pads,    │
│                             use comma to separate them. (eg. 2,3)         │
│    --with-header  -H        With header line in input file.               │
│    --columns      -c  TEXT  Sets columns for site info.                   │
│                             (Chrom,Pos,Strand)                            │
│                             [default: 1,2,3]                              │
│    --to-upper     -u        Convert motif to upper case.                  │
│    --wrap-site    -w        Wrap motif site.                              │
│    --help         -h        Show this message and exit.                   │
╰───────────────────────────────────────────────────────────────────────────╯demo:I would like to get the 2 bases before the given sites, and 3 bases after the given sites, meanwhile, wrap the give sites with bracket. Moreover, the strand information should be taken into account.use-n 2,3 -w🧫variant effectsubcommand can infer the effect of a mutationUsage: variant effect [OPTIONS]

 Annotation genomic variant effect.

╭─ Options ─────────────────────────────────────────────────────────────────╮
│ --input                 -i  TEXT     Input position file.                 │
│ --output                -o  TEXT     Output annotation file               │
│ --reference             -r  TEXT     reference species                    │
│ --reference-gtf             TEXT     Customized reference gtf file.       │
│ --reference-transcript      TEXT     Customized reference transcript      │
│                                      fasta file.                          │
│ --reference-protein         TEXT     Customized reference protein fasta   │
│                                      file.                                │
│ --release               -e  INTEGER  ensembl release                      │
│ --strandness            -s           Use strand infomation or not?        │
│ --pU-mode               -u           Make rRNA, tRNA, snoRNA into top     │
│                                      priority.                            │
│ --npad                  -n  INTEGER  Number of padding base to call       │
│                                      motif.                               │
│ --all-effects           -a           Output all effects.                  │
│ --with-header           -H           With header line in input file.      │
│ --columns               -c  TEXT     Sets columns for site info.          │
│                                      (Chrom,Pos,Strand,Ref,Alt)           │
│                                      [default: 1,2,3,4,5]                 │
│ --help                  -h           Show this message and exit.          │
╰───────────────────────────────────────────────────────────────────────────╯demo:Store the following table in file (sites.tsv).ChromPositionStrandRefAltchr1230703034-CTchr1269353439+ATchr1423645352+GTchr2215361150-ATchr284906537+CTchr2239319077-TAchr2239319095-TAchr2239319098-TARun command:variant-effect-isites.tsv-H-rhuman-e108-tRNA-H-c1,2,3-ispecify the input file-Hmeans the file is with header line, and the first row will be skipped;-ruse the specific genome, default is human-especify the Ensembl release version-cmeans only use some of the columns in the input file. default will use the first 5 columns.You will have this outputChromPositionStrandRefAltmut_typegene_typegene_namegene_postranscript_nametranscript_postranscript_motifcoding_poscodon_refaa_posaa_refdistance2splicechr1230703034-CTThreePrimeUTRprotein_codingENSG00000135744(AGT)42543ENST00000680041(AGT-208)1753TGTGTCACCCCCAGTCTCCCANoneNoneNoneNone295chr1269353439+ATThreePrimeUTRprotein_codingENSG00000090382(LYZ)5059ENST00000261267(LYZ-201)695TAGAACTAATACTGGTGAAAANoneNoneNoneNone286chr1423645352+GTThreePrimeUTRprotein_codingENSG00000100867(DHRS2)15238ENST00000344777(DHRS2-202)1391CTGCCATTCTGCCAGACTAGCNoneNoneNoneNone210chr2215361150-ATThreePrimeUTRprotein_codingENSG00000115414(FN1)74924ENST00000323926(FN1-201)8012GGCCCGCAATACTGTAGGAACNoneNoneNoneNone476chr284906537+CTThreePrimeUTRprotein_codingENSG00000034510(TMSB10)882ENST00000233143(TMSB10-201)327CCTGGGCACTCCGCGCCGATGNoneNoneNoneNone148chr2239319077-TAIntronicprotein_codingENSG00000100316(RPL3)1313ENST00000216146(RPL3-201)NoneNoneNoneNoneNoneNoneNonechr2239319095-TAIntronicprotein_codingENSG00000100316(RPL3)1295ENST00000216146(RPL3-201)NoneNoneNoneNoneNoneNoneNonechr2239319098-TAIntronicprotein_codingENSG00000100316(RPL3)1292ENST00000216146(RPL3-201)NoneNoneNoneNoneNoneNoneNone🧫variant coordinatesubcommand can mapping chrom name and positions between different reference coordinateUsage: variant coordinate [OPTIONS]

 Fetch genomic motif.

╭─ Options ───────────────────────────────────────────────────────────────────╮
│ --input              -i  TEXT  Input position file.                         │
│ --output             -o  TEXT  Output annotation file.                      │
│ --reference-mapping  -m  TEXT  Mapping file for chrom name, first column is │
│                                chrom in the input, second column is chrom   │
│                                in the reference db (sep by tab)             │
│ --buildin-mapping    -M  TEXT  Build-in mapping for chrom name: U2E (UCSC   │
│                                to Ensembl), E2U (Ensembl to UCSC)           │
│ --with-header        -H        With header line in input file.              │
│ --columns            -c  TEXT  Sets columns for site info. (Chrom)          │
│                                [default: 1]                                 │
│ --help               -h        Show this message and exit.                  │
╰─────────────────────────────────────────────────────────────────────────────╯⏳⏳⏳ more functions will be supported in the futureTODO:imporve speed. Base oncgranges,pyranges?, orBioCantor?