Fixed bug with plyranges

vsbuffalo · May 19, 2024 · d511f32 · d511f32
1 parent 3588443
commit d511f32
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Showing 2 changed files with 24 additions and 30 deletions.
diff --git a/additional_benchmarks/Snakefile b/additional_benchmarks/Snakefile
@@ -1,6 +1,6 @@
 import numpy as np
 
-RSCRIPT = "~/.conda/envs/granges_benchmark/bin/R"
+RSCRIPT = "~/.conda/envs/granges_benchmark/bin/Rscript"
 GRANGES = "../target/release/granges"
 SEQLENS = "../tests_data/hg38_seqlens.tsv"
 NREPS = 100
@@ -58,7 +58,7 @@ rule granges_filter:
  benchmark: repeat("benchmarks/granges_filter__size_{size}.tsv", NREPS)
  resources:
  partition="savio3",
- runtime=300,
+ runtime=600,
  mem_mb=96000,
  cpus_per_task=40
  shell:
@@ -72,7 +72,7 @@ rule bedtools_intersect:
  benchmark: repeat("benchmarks/bedtools_intersect__size_{size}.tsv", NREPS)
  resources:
  partition="savio3",
- runtime=300,
+ runtime=600,
  mem_mb=96000,
  cpus_per_task=40
  shell:
@@ -87,25 +87,25 @@ rule plyranges_join_overlap_inner:
  benchmark: repeat("benchmarks/plyranges_join_overlap_inner__size_{size}.tsv", NREPS)
  resources:
  partition="savio3",
- runtime=300,
+ runtime=600,
  mem_mb=96000,
  cpus_per_task=40
  shell:
  """
- {params.rscript} Rscripts/plyranges_join_overlap_inner.r {input.a} {input.b} > {output}
+ {params.rscript} rscripts/plyranges_join_overlap_inner.r {input.a} {input.b} {output}
  """
 
 ## ----- granges map / bedtools map -----
 WINDOWS = "windows/width_100000.bed"
 
 rule granges_map:
- input: right=WINDOWS, left="random_bed/scores/{size}__A.bed.gz",
+ input: left=WINDOWS, right="random_bed/scores/{size}__A.bed.gz",
  genome=SEQLENS, granges=GRANGES
  output: "results/granges_map__size_{size}.bed"
  benchmark: repeat("benchmarks/granges_map__size_{size}.tsv", NREPS)
  resources:
  partition="savio3",
- runtime=300,
+ runtime=600,
  mem_mb=96000,
  cpus_per_task=40
  shell:
@@ -114,12 +114,12 @@ rule granges_map:
  """
 
 rule bedtools_map:
- input: right=WINDOWS, left="random_bed/scores/{size}__A.bed.gz"
+ input: left=WINDOWS, right="random_bed/scores/{size}__A.bed.gz"
  output: "results/bedtools_map__size_{size}.bed"
  benchmark: repeat("benchmarks/bedtools_map__size_{size}.tsv", NREPS)
  resources:
  partition="savio3",
- runtime=300,
+ runtime=600,
  mem_mb=96000,
  cpus_per_task=40
  shell:
@@ -129,8 +129,8 @@ rule bedtools_map:
 
 rule plyranges_map:
  input:
- right=WINDOWS,
- left="random_bed/scores/{size}__A.bed.gz"
+ left=WINDOWS,
+ right="random_bed/scores/{size}__A.bed.gz"
  output:
  "results/plyranges_map__size_{size}.bed"
  benchmark:
@@ -143,7 +143,7 @@ rule plyranges_map:
  params: rscript = RSCRIPT
  shell:
  """
- {params.rscript} Rscripts/plyranges_map.r {input.left} {input.right} > {output}
+ {params.rscript} rscripts/plyranges_map.r {input.left} {input.right} {output}
  """
 
 

diff --git a/additional_benchmarks/rscripts/plyranges_map.r b/additional_benchmarks/rscripts/plyranges_map.r
@@ -1,4 +1,5 @@
 library(plyranges)
+library(rtracklayer)
 
 args <- commandArgs(trailingOnly = TRUE)
 
@@ -15,23 +16,16 @@ granges_a <- read_bed(bed_file_a)
 granges_b <- read_bed(bed_file_b)
 
 # Perform the map operation
-mapped_result <- join_overlap_left(
- granges_a,
- granges_b,
- suffix = c(".left", ".right")
-) %>%
- select(
- seqnames,
- start.left,
- end.left,
- width = width.left,
- strand,
- min = min(score.right),
- max = max(score.right),
- mean = mean(score.right),
- sum = sum(score.right),
- median = median(score.right)
+mapped_granges <- granges_a %>%
+ join_overlap_inner(granges_b) %>%
+ group_by(seqnames, start, end, strand) %>%
+ summarise(
+ min = min(score, na.rm = TRUE),
+ max = max(score, na.rm = TRUE),
+ mean = mean(score, na.rm = TRUE),
+ sum = sum(score, na.rm = TRUE),
+ median = median(score, na.rm = TRUE)
  )
 
-# Write the mapped result to a BED file
-write_bed(mapped_result, output_file)
+mapped_df <- as.data.frame(mapped_granges)
+write.table(mapped_df, file = output_file, sep = "\t", quote = FALSE, row.names = FALSE)