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B-UMMI / chewBBACA_tutorial

Step by step tutorial using chewBBACA with all necessary files and results
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How to get the cgMLST_all.tsv #5

Closed ryanjoel closed 4 years ago

ryanjoel commented 4 years ago

In the tutorial, "Now the file cgMLST_completegenomes/cgMLST.tsv can be concatenated with the allele call result from the 680 genomes results_all/results_20180202T112710/results_alleles.tsv", I don't know how to concatenate these two files to get the cgMLST_all.tsv

pedrorvc commented 4 years ago

Hello @ryanjoel,

The cgMLST_all.tsv can be found at https://github.com/B-UMMI/chewBBACA_tutorial/blob/master/analysis_all/cgMLST_all.tsv.

The concatenation of the files was achieved using the JoinProfiles module that takes as input 2 profile files. An example command is: chewBBACA.py JoinProfiles -p1 results_cg/results_(timestamp)/cgMLST_completegenomes/cgMLST.tsv -p2 results_all/results_20180202T112710/results_alleles.tsv -o cgMLST_all.tsv

The -p1 profile is the file obtained after running the ExtractCgMLST module, change the (timestamp) to the appropriate value. The -p2 profile is the file provided with the tutorial.

If you have any questions, don't hesitate to ask!

Cheers, Pedro

pedrorvc commented 4 years ago

Closing issue. We have updated the README to clarify this issue.

Feel free to reopen if you have more questions about the tutorial.