Cluster #17
Merged
Cluster #17
+107
−69
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
bin/reduce_sequence.R
Outdated
| #' @return reduced bed | ||
| #' TODO check whether jellyfish is installed | ||
| reduce_bed <- function(input, kmer = 10, motif = 10, output = "reduced.bed", threads = NULL, clean = TRUE, minoverlap_kmer = kmer - 1, minoverlap_motif = ceiling(motif / 2), min_seq_length = max(c(motif, kmer)), motif_occurence = 1) { | ||
| #' @details If there is a header supplied other then the default data.table nameing scheme ('V1', 'V2', etc.) it will be kept. |
bin/reduce_sequence.R
Outdated
| #' @param threads Number of threads. Default = 1. 0 for all cores. | ||
| #' @param input Input bed-file. Last column must be sequences. | ||
| #' @param kmer Kmer length. Default = 10 | ||
| #' @param motif Estimated motif length. Default = 10 |
There was a problem hiding this comment.
Parameter 'motif' does not contain a lot of information about its function.
Maybe it should be named something like 'estimated_motif_len'?
bin/reduce_sequence.R
Outdated
| #' @param output Output file | ||
| #' @param threads Number of threads. Default = 1. 0 for all cores. | ||
| #' @param input Input bed-file. Last column must be sequences. | ||
| #' @param kmer Kmer length. Default = 10 |
There was a problem hiding this comment.
kmer_len instead of kmer?
bin/reduce_sequence.R
Outdated
| #' @param clean Delete all temporary files. | ||
| #' @param minoverlap_kmer Minimum required overlap between kmer to merge kmer. Used to create reduced sequence ranges. Can not be greater than kmer length. Default = kmer - 1 | ||
| #' @param minoverlap_kmer Minimum required overlap between kmer. Used to create reduced sequence ranges out of merged kmer. Can not be greater than kmer length . Default = kmer - 1 |
There was a problem hiding this comment.
Typo:
- length.
- k-mers
bin/reduce_sequence.R
Outdated
| @@ -9,32 +9,41 @@ option_list <- list( | |||
| make_option(opt_str = c("-t", "--threads"), default = 1, help = "Number of threads to use. Use 0 for all available cores. Default = %default", metavar = "integer"), | |||
| make_option(opt_str = c("-c", "--clean"), default = TRUE, help = "Delete all temporary files. Default = %default", metavar = "logical"), | |||
| make_option(opt_str = c("-s", "--min_seq_length"), default = NULL, help = "Remove sequences below this length. Defaults to the maximum value of motif and kmer and can not be lower.", metavar = "integer", type = "integer"), | |||
| make_option(opt_str = c("-n", "--minoverlap_kmer"), default = NULL, help = "Minimum required overlap between kmer to merge kmer. Used to create reduced sequence ranges. Can not be greater than kmer length. Default = kmer - 1", metavar = "integer", type = "integer"), | |||
| make_option(opt_str = c("-n", "--minoverlap_kmer"), default = NULL, help = "Minimum required overlap between kmer. Used to create reduced sequence ranges out of merged kmer. Can not be greater than kmer length. Default = kmer - 1", metavar = "integer", type = "integer"), | |||
bin/cdhit_wrapper.R
Outdated
| @@ -68,24 +69,33 @@ opt <- parse_args(opt_parser) | |||
| #' @param gat_ext Gap extension score. Default = -1 (CD-HIT parameter) | |||
| #' @param sort_cluster_by_size Either sort cluster by decreasing length (= 0) or by decreasing size (= 1). Default = 1 (CD-HIT parameter) | |||
| #' | |||
| #' TODO check whether cdhit is installed | |||
| #' @details If there is a header supplied other then the default data.table nameing scheme ('V1', 'V2', etc.) it will be kept and extended. | |||
pipeline.nf
Outdated
| @@ -268,7 +268,7 @@ process overlap_with_known_TFBS { | |||
|
|
|||
| /* | |||
| */ | |||
| process reduce_bed { | |||
| process reduce_sequence { | |||
There was a problem hiding this comment.
Please add a small description to the process reduce_sequence and clustering.
renewiegandt
requested changes
Dec 19, 2018
There was a problem hiding this comment.
Found a few typos and made a few suggestions for parameter names. Apperently 'kmer' is writen k-mer you should take a look at that.
You could also add a small description for the processes reduce_sequences and clustering.
The changes in the code functionality look good to me.
renewiegandt
approved these changes
Dec 20, 2018
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.
So far the check whether the required tools are installed only works on linux. For now this should be enough but tell me if I should look into making this platform independent.