Is there a way to extract the names of closest references in the tree?

[Adi Lavy]

Hi All!

I've been using pplacer and guppy to place a set of sequences on a reference tree. The reference tree does not contain any taxonomy information, just names of organisms.

I would like to know if there is a way to ask pplacer to create a table (or list) in which for each query sequence it will show what are the N closest reference sequences.

Thank you!

Adi

[Greg G]

Hello,

I had this same question, and there is function in guppy called "to_csv" that does the job, by creating a table of best hits.

Example usage:

~/pplacer-Linux-v1.1.alpha19/guppy to_csv Input.jplace -o Output_table.csv

It helps to first run pplacer and have it to output only the top hit for each sequence (rather than up to 4 matches, as is the default). That can be done like so:

Example usage:

~/pplacer-Linux-v1.1.alpha19/pplacer -c example.refpkg aln.fasta* --keep-at-most 1

~Greg

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[Adi Lavy]

Hi Greg,

Thank you for your answer.

I did follow your advice, but I did not restrict pplacer to just 1 match as I could use the 4 matches... 

The output table has the following format:

origin,name,multiplicity,edge_num,like_weight_ratio,post_prob,likelihood,marginal_like,distal_length,pendant_length,classification,map_ratio,map_overlap,map_identity
query.15rp,Query_PLM0_60_coex_sep16_Abawaca1_113,1,2201,1,1,-5.89562e+06,-5.89563e+06,0.189797,0.192744,NA,NA,NA,NA

How can I get the actual names of the best matches from this table?

Thanks!

Adi

[Greg G]

Sorry, you're right, I see now that I have not fully addressed your question. Unfortunately I do not have an answer, as I resorted to manually replacing the branch numbers in the tree with taxon names of interest.

Wish I could be of more help,

~Greg