Closed alexvasilikop closed 1 year ago
Hi Alex,
First, thank you very much for checking out OrthoSNAP and for providing a comment. OrthoSNAP and other software would be nothing without a helpful user base—i.e., researchers like you!
Second, the issue stems from what version of OrthoSNAP you are using. The -ip
argument was not added until a later version of OrthoSNAP. A changelog of OrthoSNAP is available here: changelog, docs. To update your version of OrthoSNAP, you can use the following command: pip install orthosnap -U
.
Thanks again for using OrthoSNAP. You may find some of the other software I have developed useful for your research; here is the link in case you are interested :D https://jlsteenwyk.com/software.html.
best,
Jacob
Hello,
I am trying to invoke the option for in-paralog selection but it seems it is not recognized
$ orthosnap -f OG0000452.fa -t OG0000452_tree.txt -ip median_seq_len
orthosnap: error: unrecognized arguments: -ip median_seq_len
Also in the $orthosnap -h command there is no such option but it exists in the documentation $orthosnap -h
/ \
Version: 0.0.1 Citation: Steenwyk et al. Usage: orthosnap [optional arguments]
required arguments: -t, --tree
input tree file in newick format
-f, --fasta
input sequence file in fasta format
optional arguments: -s, --support
support threshold for bipartition collapsing
default: 80
-o, --occupancy
occupancy threshold for minimum number of tips in orthologous subgroup
default: 50 percent of total number of taxa
Detailed explanation of arguments |
-t, --tree
taxa name and gene name should be separate by a "|" symbol For example, "gene_a" from "species_a" should appear in the tree as "species_a|gene_a", and "gene_b" from "species_a" should appear in the tree as "species_a|gene_b", and so on and so forth.
-f, --fasta
taxa name and gene name should be formatted the same as in the tree file. Thus, "gene_a" from "species_a" should appear in the tree as "species_a|gene_a" and so on and so forth.
-s, --support
default value is 80 and is set for ultrafast bootstrap approximations. If bipartitions support was evaluated using standard bootstrap, a common threshold to use is 70.
-o, --occupancy
What might be the issue? Thanks Alex