Cluster #17
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Cluster #17
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bin/reduce_sequence.R
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| #' @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
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| #' @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 |
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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
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| #' @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 |
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kmer_len instead of kmer?
bin/reduce_sequence.R
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| #' @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 |
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Typo:
- length.
- k-mers
bin/reduce_sequence.R
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| @@ -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
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| @@ -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
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| @@ -268,7 +268,7 @@ process overlap_with_known_TFBS { | |||
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| /* | |||
| */ | |||
| process reduce_bed { | |||
| process reduce_sequence { | |||
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Please add a small description to the process reduce_sequence and clustering.
renewiegandt
requested changes
Dec 19, 2018
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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
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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.