Update environment information (#164)

environment.yaml

@@ -2,24 +2,42 @@ name: como
 channels:
   - bioconda
   - conda-forge
-  - r
   - gurobi
   - anaconda
-  - hcc
-  - default
 dependencies:
-  - bioconda::bioconductor-affy~=1.72.0
+  - anaconda::lxml~=4.9.1
   - bioconda::bioconductor-affyio~=1.64.0
+  - bioconda::bioconductor-affy~=1.72.0
   - bioconda::bioconductor-agilp~=3.26.0
   - bioconda::bioconductor-biomart~=2.50.0
   - bioconda::bioconductor-deseq2~=1.34.0
   - bioconda::bioconductor-edger~=3.36.0
   - bioconda::bioconductor-genefilter~=1.76.0
   - bioconda::bioconductor-hgu133acdf~=2.18.0
   - bioconda::bioconductor-limma~=3.50.1
-  - conda-forge::r-factominer~=2.8
+  - bioconda::crux-toolkit~=4.1
+  - bioconda::escher==1.7.*
+  - bioconda::thermorawfileparser~=1.4.0
+  - conda-forge::aioftp~=0.21.2
+  - conda-forge::bioservices~=1.11.2
+  - conda-forge::cobra<=1.0.0
+  - conda-forge::geoparse~=2.0.3
+  - conda-forge::git~=2.37.0
+  #  - conda-forge::jupyterlab-spreadsheet-editor==0.6.*
+  - conda-forge::jupyterlab~=4.0.0
+  - conda-forge::markupsafe~=2.0.1
+  - conda-forge::numpy~=1.23.0
+  - conda-forge::openpyxl~=3.0.10
+  - conda-forge::optlang~=1.5.2
+  - conda-forge::pandas<=3.0.0
+  - conda-forge::pip~=22.1.2
+  - conda-forge::python-libsbml~=5.19.2
+  - conda-forge::python~=3.10
+  # - conda-forge::r-base~=4
+  # - conda-forge::r-base
   - conda-forge::r-biocmanager~=1.30.18
   - conda-forge::r-devtools~=2.4.3
+  - conda-forge::r-factominer~=2.8
   - conda-forge::r-ggrepel~=0.9.1
   - conda-forge::r-irdisplay~=1.1
   - conda-forge::r-irkernel~=1.3
@@ -32,37 +50,18 @@ dependencies:
   - conda-forge::r-tidyverse~=1.3.1
   - conda-forge::r-uwot~=0.1.11
   - conda-forge::r-zoo~=1.8_10
-  - conda-forge::aioftp~=0.21.2
-  - conda-forge::bioservices~=1.11.2
-  - bioconda::crux-toolkit~=4.1
-  - conda-forge::geoparse~=2.0.3
-  - conda-forge::git~=2.37.0
-  - gurobi::gurobi~=10.0
-  - conda-forge::jupyterlab~=4.0.0
-  - anaconda::lxml~=4.9.1
-  - conda-forge::markupsafe~=2.0.1
-  - conda-forge::numpy~=1.23.0
-  - conda-forge::openpyxl~=3.0.10
-  - conda-forge::optlang~=1.5.2
-  - conda-forge::pandas~=1.4.3
-  - conda-forge::pip~=22.1.2
-  - conda-forge::python-libsbml~=5.19.2
-  - conda-forge::python~=3.10
   - conda-forge::requests~=2.28.1
   - conda-forge::rpy2~=3.5.1
   - conda-forge::scipy~=1.8.1
   - conda-forge::sqlalchemy~=1.4.39
-  - bioconda::thermorawfileparser~=1.4.0
   - conda-forge::tqdm~=4.64.1
   - conda-forge::unidecode~=1.3.4
   - conda-forge::wget~=1.20.3
   - conda-forge::xlrd~=2.0.1
+  - gurobi::gurobi~=10.0
   - pip:
       - async_bioservices
-      - cobra==0.26.*
-      - Escher==1.7.*
       - framed==0.5.*
       - memote==0.13.*
-      - jupyterlab-spreadsheet-editor==0.6.*
       - git+https://github.com/JoshLoecker/cobamp.git
       - git+https://github.com/JoshLoecker/troppo.git

main/src/rnaseq_preprocess.py

@@ -1,14 +1,11 @@
-#!/usr/bin/python3
-
-import pandas as pd
-
 import re
 import os
 import sys
 import glob
 import asyncio
 import argparse
 import numpy as np
+import pandas as pd
 from pathlib import Path
 
 import rpy2_api
@@ -307,9 +304,9 @@ async def handle_context_batch(context_names, mode, form: InputDatabase, taxon_i
                 df_m.to_excel(mwriter, sheet_name=context_name, header=True, index=False)
 
             tmatrix, mmatrix = split_counts_matrices(matrix_path_all, df_t, df_m)
-            if len(tmatrix.columns) > 1:
+            if len(tmatrix.columns) >= 1:
                 tmatrix.to_csv(matrix_path_total, header=True, index=False)
-            if len(mmatrix.columns) > 1:
+            if len(mmatrix.columns) >= 1:
                 mmatrix.to_csv(matrix_path_mrna, header=True, index=False)
 
     if mode == "make":

main/src/rscripts/rnaseq.R

@@ -51,7 +51,7 @@ read_counts_matrix <- function(counts_matrix_filepath, config_filepath, info_fil
     }
 
     # add to group count matrices and insert lists
-    for (i in 1:length(config_object$SampleName)) {
+    for (i in seq_along(config_object$SampleName)) {
         entry <- config_object$SampleName[i]  # CELL-TYPE_S##R##
         group <- config_object$Group[i]