merge command

[Michael Doane]

Hi all,

Using the 'merge' command, does information about where each query originates remain after .jplace files are merged? I'd like draw a tree that indicates where within the tree each file places its sequences.

Thanks in advance.

Mike

[Erick Matsen]

It does not. 

However, take a look at https://matsen.github.io/pplacer/generated_rst/guppy_merge.html#guppy-merge 

There you can see that the --split-csv option writes out a csv file indicating the source of each read in the combined placefile. You can then use those as described in the "split placefile" section of the guppy manual. 

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Frederick "Erick" Matsen, Associate Member
Fred Hutchinson Cancer Research Center
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[Michael Doane]

Hi Erick,

Thank you for the assistance. I am attempting running the --split-csv flag with the 'merge' command. I am not having luck generating the .csv file.

Here is the command used:

~/phylosift_v1.0.1/bin/./guppy merge -o ws_1_2.jplace --out-dir ~/temp/ --prefix test --split-csv ~/phylogenetic_diversity/jplace/shark/ws_3.fastq.gz.jplace ~/phylogenetic_diversity/jplace/shark/ws_4.fastq.gz.jplace

The command generates the merged .jplace with the correct output name, prefix appended, and to the indicated directory. The csv however it not generated.

Thanks in advance.

Mike

[Erick Matsen]

I haven't done this in a while but it looks to me that 

--split-csv ~/phylogenetic_diversity/jplace/shark/ws_3.fastq.gz.jplace

will write a CSV file to ~/phylogenetic_diversity/jplace/shark/ws_3.fastq.gz.jplace . I doubt this is what you intended.