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Pipelines creating allelic presence-absence matrices from SRST2 and ARIBA results

License: GNU General Public License v3.0

Python 51.13% R 41.71% Shell 7.15%

gene-detection ariba presence-absence-matrix genotyping antimicrobial-resistance

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pammaker's Issues

Change allele names to lowercase

It is not correct to use uppercase letters for leading allele names, although this format is used in the original ARG-ANNOT database.

Support sequence clustering under a nucleotide identity less than 100%

For example, to allow a given number of SNVs and truncations.

Error with dataframe in filter_allele_table.R

Hi and Thank you for this great software.
Unfortunately I am having a problem in the checking reliability of SRST2 allele calling. I am using a pubmlst 7 allele protocol. When running the R script I get :
Rscript /home/me/PAMmaker/reliability/filter_allele_table.R --profiles summary__compiledResults.txt --scores mergedScores__gene.scores --output Pan_srst2__reliableCalls
Error in [.data.frame(x, , c(1, (which(names(x) == "maxMAF") + 1):ncol(x))) :
undefined columns selected
Calls: rmMLST -> [ -> [.data.frame
When I look at the columns they are :
Sample ST glpF sigF glpT Natrans rpoB ftsA clpC mismatches uncertainty depth maxMAF
Do I need to remove some columns or rename them?

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