Merge pull request #44 from Arcadia-Science/ter/cleanup-envs

Cleanup unused envs, scripts, and file pointers
Arcadia-Science · May 22, 2024 · 38782b9 · 38782b9
2 parents c55c79a + 6fd32b2
commit 38782b9
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Showing 5 changed files with 1 addition and 49 deletions.
diff --git a/curate_datasets_and_build_models.snakefile b/curate_datasets_and_build_models.snakefile
@@ -12,7 +12,7 @@ VALIDATION_TYPES = [
 # Note that for variables CODING_TYPES and DATASET_TYPES, the order matters;
 # The snakemake expand() function maintains the order of these arguments.
 # This behavior is used later in the snakefile to specify inputs and outputs of different scripts/shell commands.
-# The order of CODING_TYPES must correspond to the order of the positional args that are later passed to rnasamba.
+# The order of CODING_TYPES must correspond to the order of the positional args that are later passed to plm-utils.
 # In addition, the order of CODING_TYPES and DATASET_TYPES is used to declare outputs in the rule/R script process_sequences_into_nonoverlapping_sets.
 CODING_TYPES = ["coding", "noncoding"]
 DATASET_TYPES = ["train", "validation"]

diff --git a/envs/caret.yml b/envs/caret.yml
diff --git a/envs/rnasamba.yml b/envs/rnasamba.yml
diff --git a/scripts/calculate_rnasamba_model_accuracy.R b/scripts/calculate_rnasamba_model_accuracy.R
diff --git a/scripts/calculate_sequence_statistics.R b/scripts/calculate_sequence_statistics.R
@@ -2,7 +2,6 @@ library(tidyverse)
 source("scripts/parse_sequence_information.R")
 
 files <- unlist(snakemake@input)
-#files <- Sys.glob("outputs/models/rnasamba/build/2_sequence_sets/*.fa.seqkit.fai")
 fai_col_names <- c("sequence", "length", "offset", "linebases", "linewidth")
 fai <- files %>%
   set_names() %>%