Improved: Motif clustering #39
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
HendrikSchultheis
changed the title
HendrikSchultheis
requested changes
Jan 6, 2019
| @@ -1,13 +1,13 @@ | |||
| #!/usr/bin/env Rscript | |||
| library("optparse") | |||
| if (!require(optparse)) install.packages("optparse"); library(optparse) | |||
|
|
|||
| option_list <- list( | |||
| make_option(opt_str = c("-i", "--input"), default = NULL, help = "Input bed-file. Second last column must be sequences and last column must be the cluster_id.", metavar = "character"), | |||
There was a problem hiding this comment.
cluster_id -> cluster id
|
|
||
| option_list <- list( | ||
| make_option(opt_str = c("-i", "--input"), default = NULL, help = "Input bed-file. Second last column must be sequences and last column must be the cluster_id.", metavar = "character"), | ||
| make_option(opt_str = c("-p", "--prefix"), default = "" , help = "Prefix for file names. Default = '%default'", metavar = "character"), | ||
| make_option(opt_str = c("-m", "--min_seq"), default = 100, help = "Minimum amount of sequences in clusters. Default = %default", metavar = "integer") | ||
| ) | ||
|
|
||
| opt_parser <- OptionParser(option_list = option_list, | ||
| opt_parser <- OptionParser(option_list = option_list, | ||
| description = "Convert BED-file to one FASTA-file per cluster") |
There was a problem hiding this comment.
Author and email are missing.
|
|
||
| option_list <- list( | ||
| make_option(opt_str = c("-i", "--input"), default = NULL, help = "Input bed-file. Second last column must be sequences and last column must be the cluster_id.", metavar = "character"), | ||
| make_option(opt_str = c("-p", "--prefix"), default = "" , help = "Prefix for file names. Default = '%default'", metavar = "character"), | ||
| make_option(opt_str = c("-m", "--min_seq"), default = 100, help = "Minimum amount of sequences in clusters. Default = %default", metavar = "integer") | ||
| ) | ||
|
|
||
| opt_parser <- OptionParser(option_list = option_list, | ||
| opt_parser <- OptionParser(option_list = option_list, | ||
| description = "Convert BED-file to one FASTA-file per cluster") | ||
|
|
||
| opt <- parse_args(opt_parser) |
There was a problem hiding this comment.
The Sequences of each cluster are written as an FASTA-file.
| if (is.null(bedInput)) { | ||
| stop("ERROR: Input parameter cannot be null! Please specify the input parameter.") | ||
| } | ||
|
|
||
| bed <- data.table::fread(bedInput, sep = "\t") | ||
|
|
||
|
|
||
| # Get last column of data.table, which refers to the cluster, as a vector. | ||
| cluster_no <- as.vector(bed[[ncol(bed)]]) |
There was a problem hiding this comment.
You can remove as.vector. Using [[]] already returns a vector.
| # Split data.table bed on its last column (cluster_no) into list of data.frames | ||
| clusters <- split(bed, cluster_no, sorted = TRUE, flatten = FALSE) | ||
|
|
||
| # For each data.frame(cluster) in list clusters: | ||
| discard <- lapply(1:length(clusters), function(i){ |
There was a problem hiding this comment.
It's nicer to use seq_len instead of 1:x.
| #' @contact rene.wiegandt(at)mpi-bn.mpg.de | ||
| merge_similar <- function(tsv_in, file_list, min_weight){ | ||
|
|
||
| files <- unlist(as.list(strsplit(file_list, ","))) |
There was a problem hiding this comment.
The as.list is redundant strsplit already returns a list.
|
|
||
| # split the string on the character "." in the first to columns and safe the last value each, to get the number of the cluster. | ||
| tsv <- data.table::fread(tsv_in, header = TRUE, sep = "\t",colClasses = 'character') | ||
| query_cluster <- unlist(lapply(strsplit(tsv[["Query_ID"]],"\\."), function(l){ |
There was a problem hiding this comment.
Use vapply instead it already returns a vector.
| tail(l,n=1) | ||
| })) | ||
|
|
||
| # create data.table with only the cluster-numbers |
There was a problem hiding this comment.
You don't have to convert later if you create your data.table with numeric columns right away.
| sim_not_unique[, query_cluster := as.numeric(query_cluster)] | ||
| sim_not_unique[, target_cluster := as.numeric(target_cluster)] | ||
|
|
||
| # remove rows if column 1 is idential to column 2 |
| system(paste("cat",f,">",basename(f))) | ||
| }) | ||
| } | ||
| # merge FASTA-files depending on the clustered graphs |
There was a problem hiding this comment.
One or two more comments would be nice in this lapply.
|
Link #16 |
Sign in
to join this conversation on GitHub.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Improved motif clustering by comparing the motifs of each cluster separately with the merged motif file.
Added new R-script which labels the TSV-files with the corresponding cluster ID.