Comments (9)
Hi Jorge,
Thanks very much for your question. The idea of running multiple taxa has been floated before and I have created a stub in the code to do just that. I just haven't had the time to fully implement it. Also, there may be an issue as phylota was conceived to work hierarchically with the taxonomy, it takes each taxon ID, looks for descendants and tries to find clusters within them. If you have multiple single species each, with few or no descendants, it may not work because it can't find any clusters within those descendants.
Could you send me a snippet of the code you wish to work?
Thanks,
Dom
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Hi Dom,
I see, so in the case that I am interested in only few species, do you recommend me to download the complete group where the species are?
This is a snippet of the code that I would like to use:
[id_ncbi.txt](https://github.com/AntonelliLab/phylotaR/files/1929349/id_ncbi.txt)
ferns<-read.csv("~id_ncbi.txt")
wd <- "..."
ncbi_dr <- "..."
txid <- ferns$id
setUp(wd=wd, txid=txid, ncbi_dr=ncbi_dr)
run(wd=wd)
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Hi Jorge,
I would suggest running it for a higher taxonomic group and then filtering out to just your chosen species. Although as you only have a few species, this is like taking a sledgehammer to a crack a nut. I'm envisaging a solution in my head, but it would take a bit of new development. I'll let you know when I get to it.
Thanks,
Dom
from phylotar.
Hi Dom,
Thanks for you advice and your support.
Best,
Jorge
from phylotar.
Update
Currently implemented a simple solution to having multiple taxonomic IDs. Avaialble via the multiple_ids
branch.
Install with ....
devtools::install_github('ropensci/phylotaR', ref = 'multiple_ids')
Tested so....
ncbi_dr <- '/usr/bin/'
wd <- 'aotus_aloutta'
setup(wd = wd, txid = c('9504', '9499'), ncbi_dr = ncbi_dr, v = TRUE)
run(wd)
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@DomBennett
I am trying to use this branch, but it seems to break if there are more than 100 input NCBI IDs. Is this easy to fix?
This fails:
o_ids = c(180203, 103653, 103646, 190150, 180214, 103633, 30253, 103640, 355377, 156590, 6997, 1164880, 519494, 7007, 58602, 1034420, 1034424, 1034413, 1034430, 103655, 156592, 168705, 168706, 169091, 461299, 461303, 62746, 13551, 37639, 58560, 355390, 1034393, 294303, 270253, 7005, 243007, 58562, 1224100, 334752, 1045891, 294298, 294301, 910373, 355388, 294342, 420843, 1323534, 441217, 85156, 294354, 420844, 1007316, 656900, 58607, 1678041, 441230, 473660, 494438, 494379, 150816, 515599, 58615, 294352, 660956, 294351, 396409, 302092, 109886, 473763, 433472, 499829, 7019, 355409, 660961, 355397, 1654701, 288127, 215059, 58594, 420850, 62794, 65742, 37261, 96519, 672150, 1312898, 116142, 1045884, 122969, 355363, 355370, 1034930, 1034436, 433447, 499840, 7004, 433444, 433445, 433443, 243009, 1038060, 319231, 863395, 1661872, 431551, 57095, 396431, 795156, 274599, 227609, 1634087, 7010, 361523)
blast_dir = '/usr/local/Cellar/blast/2.9.0/bin'
work_dir = './Orthoptera'
dir.create(path = work_dir,showWarnings = F)
phylotaR::setup(wd = work_dir,
txid = o_ids,
ncbi_dr = blast_dir,
v = TRUE,
overwrite = TRUE)
phylotaR::run(work_dir)
resulting in
---------------------------------------------------
Running pipeline on [unix] at [2019-12-02 10:02:14]
---------------------------------------------------
Running stages: taxise, download, cluster, cluster2
--------------------------------------------
Starting stage TAXISE: [2019-12-02 10:02:14]
--------------------------------------------
Searching taxonomic IDs ...
Downloading taxonomic records ...
. [1-100]
. [101-131]
Extra look-up for multi-ids ...
Unexpected Error in slot(object = x, name = "lng") :
cannot get a slot ("lng") from an object of type "NULL"
Occurred [2019-12-02 10:02:27]
Contact package maintainer for help.
Error in stages_run(wd = wd, frm = 1, to = nstages, stgs_msg = stgs_msg) :
Unexpected Error in slot(object = x, name = "lng") :
cannot get a slot ("lng") from an object of type "NULL"
Occurred [2019-12-02 10:02:27]
Contact package maintainer for help.
But if I subset o_ids
to any vector with up to 100 elements, it works.
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Hi @brunoasm
This branch has been merged with the master branch and has since been updated there.
Try installing the latest master branch and try again.
Dom
from phylotar.
Thanks @DomBennett! Taxise works now.
from phylotar.
For info, we're looking for a new maintainer / a new maintainer team for this package, see #57 and feel free to volunteer, we'd be happy to help.
from phylotar.
Related Issues (20)
- problem with the restez/phylota integration
- Possibility to supply NCBI API key when running pipeline to access NCBI data faster? HOT 1
- Use phylotaR for retrieving orthologous protein sequences HOT 1
- No periods or tildes in file paths HOT 3
- Multiple markers/loci per cluster issue HOT 4
- Can not install the package in windows HOT 2
- Clusters with different parent number but the same MAD, seed, length, n_taxa, n_seqs
- Description - not enough information
- New Maintainer Wanted HOT 5
- Next release HOT 6
- CRAN archive of package outsider
- Fix pkgdown configuration for reference HOT 3
- No need for restez_connect() HOT 1
- Remove treeman as a dependency? HOT 2
- Could get something new from https://github.com/pachterlab/gget
- test failure HOT 1
- Generating taxonomic dictionary error HOT 1
- Fetch and error seem to be stuck HOT 2
- drop taxa functionality HOT 1
- Identical clusters making it into alignments HOT 1
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