ChangqingW
commented
7 months ago The pipeline functions now take arguments minimap2 and k8, the paftools.js script is included in FLAMES. Hopefully this will make it easier to run on Ubuntu.
If you would like to install the latest commit you will need to either have bioconductor in development mode (which requires R 4.4) or apply the following patch with git apply patch.txt to remove changes specific to next biocondcutor release:
diff --git a/DESCRIPTION b/DESCRIPTION
index fcb769f..cfc1578 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -39,7 +39,6 @@ Imports:
DropletUtils,
GenomicRanges,
GenomicFeatures,
- txdbmaker,
GenomicAlignments,
GenomeInfoDb,
ggplot2,
diff --git a/NAMESPACE b/NAMESPACE
index 561d2c6..2fc6eec 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -46,6 +46,7 @@ importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicAlignments,seqnames)
importFrom(GenomicFeatures,extractTranscriptSeqs)
+importFrom(GenomicFeatures,makeTxDbFromGFF)
importFrom(GenomicFeatures,transcripts)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
@@ -167,8 +168,6 @@ importFrom(tidyr,as_tibble)
importFrom(tidyr,gather)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
-importFrom(txdbmaker,makeTxDbFromGFF)
-importFrom(txdbmaker,makeTxDbFromGRanges)
importFrom(utils,file_test)
importFrom(utils,modifyList)
importFrom(utils,read.csv)
diff --git a/R/find_isoform.R b/R/find_isoform.R
index bc5db79..9f7f877 100644
--- a/R/find_isoform.R
+++ b/R/find_isoform.R
@@ -141,8 +141,7 @@ find_isoform_flames <- function(annotation, genome_fa, genome_bam, outdir, confi
#' @return Path to the outputted transcriptome assembly
#'
#' @importFrom Biostrings readDNAStringSet writeXStringSet
-#' @importFrom GenomicFeatures extractTranscriptSeqs
-#' @importFrom txdbmaker makeTxDbFromGFF
+#' @importFrom GenomicFeatures extractTranscriptSeqs makeTxDbFromGFF
#' @importFrom Rsamtools indexFa
#' @importFrom utils write.table
#'
@@ -172,7 +171,7 @@ annotation_to_fasta <- function(isoform_annotation, genome_fa, outdir, extract_f
dna_string_set <- Biostrings::readDNAStringSet(genome_fa)
names(dna_string_set) <- gsub(" .*$", "", names(dna_string_set))
- txdb <- txdbmaker::makeTxDbFromGFF(isoform_annotation)
+ txdb <- GenomicFeatures::makeTxDbFromGFF(isoform_annotation)
if (missing(extract_fn)) {
tr_string_set <- GenomicFeatures::extractTranscriptSeqs(dna_string_set, txdb,
use.names = TRUE)
diff --git a/R/model_decay.R b/R/model_decay.R
index 075cee0..d797339 100644
--- a/R/model_decay.R
+++ b/R/model_decay.R
@@ -4,7 +4,6 @@
#' that only differ by the 5' / 3' end. This could be useful for plotting average
#' coverage plots.
#'
-#' @importFrom txdbmaker makeTxDbFromGFF makeTxDbFromGRanges
#' @importFrom rtracklayer import
#' @importFrom S4Vectors split
#' @importFrom GenomicRanges strand
@@ -27,11 +26,11 @@
filter_annotation <- function(annotation, keep = "tss_differ") {
if (is.character(annotation)) {
annotation <- annotation |>
- txdbmaker::makeTxDbFromGFF() |>
+ GenomicFeatures::makeTxDbFromGFF() |>
GenomicFeatures::transcripts()
} else {
annotation <- annotation |>
- txdbmaker::makeTxDbFromGRanges() |>
+ GenomicFeatures::makeTxDbFromGRanges() |>
GenomicFeatures::transcripts()
}
@@ -55,7 +54,7 @@ filter_annotation <- function(annotation, keep = "tss_differ") {
#' @description Plot the average read coverages for each length bin or a
#' perticular isoform
#'
-#' @importFrom GenomicFeatures transcripts
+#' @importFrom GenomicFeatures makeTxDbFromGFF transcripts
#' @importFrom GenomicAlignments readGAlignments seqnames
#' @importFrom GenomicRanges width strand granges coverage
#' @importFrom Rsamtools ScanBamParam
nick-youngblut
If minimap2 is installed in a linux OS via
apt-get, the executable is located at/usr/bin/minimap2, and so "k8 and/or paftools.js" are not located in that directory.It appears that the linux package does not include paftools or k8:
So, it would be helpful to warn users that minimap2 installed via
apt-getdoes not work with FLAMES -- at least unless K8 or paftools.js is installed separately.I'm using FLAMES 1.8.0.