Question: I am trying to run stitchr in R. For programs that run in Python, I use reticulate. I create a conda environment named r-reticulate, where I want to install stitchr and run it. I try the following: if (!('r-reticulate' %in% reticulate::conda_list()[,1])){ reticulate::conda_create(envname = 'r-reticulate', packages = 'python=3.10') } reticulate::use_condaenv('r-reticulate') reticulate::py_install("stitchr", pip = TRUE) system("stitchr -h") # this does not work  But obviously enough, the system() call does not work, with the message error in running command. What would be the right way to do this? I had success in the past with anndata, for example. But this is an R package wrapper, so I can just do: reticulate::use_condaenv('r-reticulate') reticulate::py_install("anndata", pip = TRUE) data_h5ad <- anndata::read_h5ad("file.h5ad")  How can I approach the stitchr case? EDIT: So I retrieved stitchr.py location during the package installation: /usr/local/Caskroom/miniconda/base/envs/r-reticulate/lib/python3.10/site-packages/Stitchr/stitchr.py I tried all the following but nothing works (see error messages): pyloc="/usr/local/Caskroom/miniconda/base/envs/r-reticulate/lib/python3.10/site-packages/Stitchr/stitchr.py" reticulate::source_python(pyloc)   Error in py_run_file_impl(file, local, convert) : ImportError: attempted relative import with no known parent package Run reticulate::py_last_error() for details.  reticulate::py_run_file(pyloc)   Error in py_run_file_impl(file, local, convert) : ImportError: attempted relative import with no known parent package Run reticulate::py_last_error() for details.  reticulate::py_run_string(paste(pyloc, "-h"))   Error in py_run_string_impl(code, local, convert) : File "", line 1 /usr/local/Caskroom/miniconda/base/envs/r-reticulate/lib/python3.10/site-packages/Stitchr/stitchr.py -h SyntaxError: invalid syntax Run reticulate::py_last_error() for details.  I am absolutely clueless on how to proceed here.

Answer: Here is maybe what you expect. shell: conda create --name=testenv python # or conda create --name=testenv python==3.10.13 if you want a specific version for jupyter for example conda activate testenv # to be sure which pip is: whereis pip   ~/anaconda3/envs/testenv/bin/pip  shell stitchr part, read from the doc of stitchr pip install stitchr IMGTgeneDL stitchrdl stitchr -v TRBV7-3*01 -j TRBJ1-1*01 -cdr3 CASSYLQAQYTEAFF  It works with command line. shell cd ~ cp /home/extraits/anaconda3/envs/testenv/bin/stitchr ~/teststitchr.py ./teststitchr.py -v TRBV7-3*01 -j TRBJ1-1*01 -cdr3 CASSYLQAQYTEAFF  It works with command line. Create ~/teststitchr2.py filled by the content of https://jamieheather.github.io/stitchr/importing.html ~/teststitchr2.py: # import stitchr from Stitchr import stitchrfunctions as fxn from Stitchr import stitchr as st # specify details about the locus to be stitched chain = 'TRB' species = 'HUMAN' # initialise the necessary data tcr_dat, functionality, partial = fxn.get_imgt_data(chain, st.gene_types, species) codons = fxn.get_optimal_codons('', species) # provide details of the rearrangement to be stitched tcr_bits = {'v': 'TRBV7-3*01', 'j': 'TRBJ1-1*01', 'cdr3': 'CASSYLQAQYTEAFF', 'l': 'TRBV7-3*01', 'c': 'TRBC1*01', 'skip_c_checks': False, 'species': species, 'seamless': False, '5_prime_seq': '', '3_prime_seq': '', 'name': 'TCR'} # then run stitchr on that rearrangement stitched = st.stitch(tcr_bits, tcr_dat, functionality, partial, codons, 3, '') print(stitched) # Which produces (['TCR', 'TRBV7-3*01', 'TRBJ1-1*01', 'TRBC1*01', 'CASSYLQAQYTEAFF', 'TRBV7-3*01(L)'], 'ATGGG snip snip snip snip snip snip TTC', 0)  python in the shell python ./teststitchr2.py   (['TCR', 'TRBV7-301', 'TRBJ1-101', 'TRBC101','CASSYLQAQYTEAFF','TRBV7-301(L)'],'ATG snip snip snip snip TTC', 0)  In R: library(reticulate) reticulate::use_condaenv('testenv') py_run_file(file.path(path.expand('~'),'teststitchr2.py')) names(py)  reticulate::py_run_file() populates the variable py: https://rstudio.github.io/reticulate/articles/calling_python.html#executing-code Here is, by names(py), all functions and variables from reticulate prefixed by py$  c("chain", "codons", "functionality", "fxn", "partial", "r", "species", "st", "stitched", "tcr_bits", "tcr_dat")  In R: print(py$stitched )  It works :) [[1]] [1] "TCR" "TRBV7-3*01" "TRBJ1-1*01" "TRBC1*01" [5] "CASSYLQAQYTEAFF" "TRBV7-3*01(L)" [[2]] [1] "ATGGGCAC snip snip snip snip " [[3]] [1] 0  You can type myvar=py$stitched to have it in a variable and use it later. You can also try this: In R: tcr_bits2= list(v = "TRBV7-3*01", j = "TRBJ1-1*01", cdr3 = "CASSYLQAQYTEAFF", l = "TRBV7-3*01", c = "TRBC1*01", skip_c_checks = FALSE, species = "HUMAN", seamless = FALSE, `5_prime_seq` = "", `3_prime_seq` = "", name = "TCR") py$st$stitch(tcr_bits2, py$tcr_dat,py$functionality, py$partial, py$codons, 3, '')    'TCR''TRBV7-301''TRBJ1-101''TRBC101''CASSYLQAQYTEAFF''TRBV7-301(L)' 'ATG snip snip snip snip ATTTC' 0   Be careful I mixed R variable, tcr_bits2, and reticulate environment (py$). You can type myvar2=py$st$stitch(bla bla) to have it in a variable and use it later. It works again :) Edit: And a bad trick, in the Python side, if you have an issue of import, before from Stitchr import import os os.chdir(os.path.join(os.path.expanduser('~'), 'anaconda3/envs/testenv/lib/python3.12/site-packages'))  But look at also How can I import a module dynamically given the full path? This trick (os.chdir()) is only for test, but try to not use it.