Virome taxonomic profiling using BLAST

public public 1yr ago Version: v0.4 0 bookmarks
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blast-virome
blast-virome
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Snakemake workflow for virome taxonomic profiling using BLAST. It's a subworkflow based on hivlab/discover-virome, uses assembled contigs as input.

Code Snippets

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shell:
    "(get_species_taxids.sh -t {params.taxid} > {output} || true)"
SnakeMake From line 18 of rules/blast.smk 
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run:
    tab = concatenate_tables(input, sep=",", cols_to_integer=params.ranks)
    mask = tab.superkingdom == VIRUSES_TAXID
    mask = mask.fillna(False)
    vir = tab[mask]
    non_vir = tab[~mask]
    vir.to_csv(output.viral, index=False)
    non_vir.to_csv(output.non_viral, index=False)
SnakeMake From line 175 of rules/blast.smk 
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shell:
    "cat {input} > {output}"
SnakeMake From line 194 of rules/blast.smk 
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shell:
    """
    RepeatMasker {params.extra} -pa {threads} {input} -dir {params.outdir}
    if head -n 1 {output.out} | grep -q 'There were no repetitive sequences detected'; then
        ln -sr {input} {output.masked} && touch {output.tbl}
    fi
    """
SnakeMake RepeatMasker From line 37 of rules/mask.smk 
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shell:
    "python -u scripts/fix_fasta.py --input {input[0]} --output {output[0]}"
SnakeMake From line 31 of main/Snakefile
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/hivlab/blast-virome
Name: blast-virome
Version: v0.4
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Copyright: Public Domain
License: None
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