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This repository was archived by the owner on Mar 29, 2022. It is now read-only.
This repository was archived by the owner on Mar 29, 2022. It is now read-only.

"path file" for -names, -nodes, -acc2tax etc #6

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@tpinotti

is it possible to to make metadamage read a file containing the path for "-names", "-nodes", "-acc2tax" (like one per line) instead of us having to list it on the command? I am thinking that you will more or less use the same paths every time, so if you just have a .txt file ("ncbi.tax") with those paths, you can do:

metadamage merge file.lca file.bdamage.gz -t ncbi.tax -howmany 15 > file.merged.lca
OR
metadamage lca -simscorelow 0.95 -simscorehigh 1.0 -t ncbi.tax -bam file.bam -outnames file -lca_rank genus -minmapq 30 -howmany 15

instead of

metadamage merge file.lca file.bdamage.gz -names /willerslev/users-shared/science-snm-willerslev-npl206/ngsLCA/ngsLCA/ncbi_tax_dump_files/names.dmp.gz -nodes /willerslev/users-shared/science-snm-willerslev-npl206/ngsLCA/ngsLCA/ncbi_tax_dump_files/nodes.dmp.gz -howmany 15 > file.merged.lca
OR
metadamage lca -simscorelow 0.95 -simscorehigh 1.0 -names /willerslev/users-shared/science-snm-willerslev-npl206/ngsLCA/ngsLCA/ncbi_tax_dump_files/names.dmp.gz -nodes /willerslev/users-shared/science-snm-willerslev-npl206/ngsLCA/ngsLCA/ncbi_tax_dump_files/nodes.dmp.gz -acc2tax /willerslev/users-shared/science-snm-willerslev-zsb202/soft/ngslca/accession2taxid/combined_taxid_accssionNO_20200425.gz -bam file.bam -outnames file -lca_rank genus -minmapq 30 -howmany 15

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