mnshgl0110 / hometools Goto Github PK

usage: Collections of command-line functions to perform common pre-processing and analysis functions.
       [-h]
       {getchr,sampfa,exseq,getscaf,seqsize,filsize,subnuc,basrat,genome_ranges,get_homopoly,asstat,shannon,fachrid,faline,bamcov,pbamrc,splitbam,mapbp,bam2coords,ppileup,runsyri,syriidx,plthist,plotal,pltbar,asmreads,gfatofa,gfftrans,gffsort,vcfdp,getcol,smprow}
       ...

positional arguments:
  {getchr,sampfa,exseq,getscaf,seqsize,filsize,subnuc,basrat,genome_ranges,get_homopoly,asstat,shannon,fachrid,faline,bamcov,pbamrc,splitbam,mapbp,bam2coords,ppileup,runsyri,syriidx,plthist,plotal,pltbar,asmreads,gfatofa,gfftrans,gffsort,vcfdp,getcol,smprow}
    getchr              FASTA: Get specific chromosomes from the fasta
                        file
    sampfa              FASTA: Sample random sequences from a fasta
                        file
    exseq               FASTA: extract sequence from fasta
    getscaf             FASTA: generate scaffolds from a given
                        genome
    seqsize             FASTA: get size of dna sequences in a fasta
                        file
    filsize             FASTA: filter out smaller molecules
    subnuc              FASTA: Change character (in all sequences) in the
                        fasta file
    basrat              FASTA: Calculate the ratio of every base in the
                        genome
    genome_ranges       FASTA: Get a list of genomic ranges of a given
                        size
    get_homopoly        FASTA: Find homopolymeric regions in a given
                        fasta file
    asstat              FASTA: Get N50 values for the given list of
                        chromosomes
    shannon             FASTA: Get Shanon entropy across the length of
                        the chromosomes using sliding windows
    fachrid             FASTA: Change chromosome IDs
    faline              FASTA: Convert fasta file from single line to
                        multi line or vice-versa
    bamcov              BAM: Get mean read-depth for chromosomes from a BAM
                        file
    pbamrc              BAM: Run bam-readcount in a parallel manner by
                        dividing the input bed file.
    splitbam            BAM: Split a BAM files based on TAG value. BAM file
                        must be sorted using the TAG.
    mapbp               BAM: For a given reference coordinate get the
                        corresponding base and position in the reads/segments
                        mapping the reference position
    bam2coords          BAM: Convert BAM/SAM file to alignment coords
    ppileup             BAM: Currently it is slower than just running mpileup
                        on 1 CPU. Might be possible to optimize later. Run
                        samtools mpileup in parallel when pileup is required
                        for specific positions by dividing the input bed file.
    runsyri             syri: Parser to align and run syri on two
                        genomes
    syriidx             syri: Generates index for syri.out. Filters non-
                        SR annotations, then bgzip, then tabix index
    plthist             Plot: Takes frequency output (like from uniq -c) and
                        generates a histogram plot
    plotal              Plot: Visualise pairwise-whole genome alignments
                        between multiple genomes
    pltbar              Plot: Generate barplot. Input: a two column file with
                        first column as features and second column as values
    asmreads            GFA: For a given genomic region, get reads that
                        constitute the corresponding assembly graph
    gfatofa             GFA: Convert a gfa file to a fasta file
    gfftrans            GFF: Get transcriptome (gene sequence) for all genes
                        in a gff file. WARNING: THIS FUNCTION MIGHT HAVE BUGS.
    gffsort             GFF: Sort a GFF file based on the gene start positions
    vcfdp               VCF: Get DP and DP4 values from a VCF file.
    getcol              Table:Select columns from a TSV or CSV file using
                        column names
    smprow              Table:Select random rows from a text file

optional arguments:
  -h, --help            show this help message and exit