From 5ea4a89ec449d2d56b57718f58f1de8b10658e82 Mon Sep 17 00:00:00 2001 From: AngryMaciek Date: Wed, 20 Mar 2024 17:14:55 +0100 Subject: [PATCH] cleanup --- modules/CREATE_SITECOUNT_MATRICES/Snakefile | 15 ++++++--------- .../CREATE_SITECOUNT_MATRICES/configs/config.yml | 6 ++---- .../profiles/local-conda/config.yaml | 2 +- 3 files changed, 9 insertions(+), 14 deletions(-) diff --git a/modules/CREATE_SITECOUNT_MATRICES/Snakefile b/modules/CREATE_SITECOUNT_MATRICES/Snakefile index 9b83f1a..e557159 100755 --- a/modules/CREATE_SITECOUNT_MATRICES/Snakefile +++ b/modules/CREATE_SITECOUNT_MATRICES/Snakefile @@ -97,19 +97,16 @@ def CSM_get_abspath(p): """ return(p if p[0] == os.sep else os.path.abspath(p)) - - - - -def CSM_helper(wildcards): +def CSM_region_helper(wildcards): + """ + Helper function to determine wheter a region is supposed to be + analyzed in full or over windows + """ if wildcards.CSM_region_id in config["CSM_regions_files"]: return config["CSM_regions_files"][wildcards.CSM_region_id] else: return config["CSM_additional_regions_files"][wildcards.CSM_region_id] - - - ############################################################################## ### Target rule with final output of the pipeline ############################################################################## @@ -201,7 +198,7 @@ rule CSM_extract_window_coord_and_sequence: "{CSM_outdir}", "CSM_outdir" ), - BED_region = lambda wildcards: CSM_helper(wildcards), + BED_region = lambda wildcards: CSM_region_helper(wildcards), FASTA_genome = config["CSM_genomic_sequence"], SCRIPT_ = os.path.join( config["CSM_scripts_dir"], diff --git a/modules/CREATE_SITECOUNT_MATRICES/configs/config.yml b/modules/CREATE_SITECOUNT_MATRICES/configs/config.yml index 0966593..e9020f7 100755 --- a/modules/CREATE_SITECOUNT_MATRICES/configs/config.yml +++ b/modules/CREATE_SITECOUNT_MATRICES/configs/config.yml @@ -37,9 +37,7 @@ CSM_regions_files: # paths to the bed-formatted additional whole regions CSM_additional_regions_files: - "3pUTR_minlen150_prefix": "/data/scc2/ag-gruber-ext/wsciekly.maciek/mapp-stability-analysis/singular-sites-margin25-minutrlen150/clean-sites-prefix-UTR.bed" - "3pUTR_minlen150_total": "/data/scc2/ag-gruber-ext/wsciekly.maciek/mapp-stability-analysis/singular-sites-margin25-minutrlen150/clean-sites-total-UTR.bed" - "3pUTR_minlen150_suffix": "/data/scc2/ag-gruber-ext/wsciekly.maciek/mapp-stability-analysis/singular-sites-margin25-minutrlen150/clean-sites-suffix-UTR.bed" + "3pUTR_minlen150_total": "/data/scc2/ag-gruber-ext/MAPP_paper/supplementary_package/mapp-stability-analysis-BACKUP/singular-sites-margin25-minutrlen150/clean-sites-total-UTR.bed" # sliding window configuration: window size and slide step CSM_window_size: "50" @@ -51,7 +49,7 @@ CSM_matrix_type: "kmers" # options for "kmers" sitecount matrices: # inclusive ends specification for the range of k-mers sizes = [kmer_min,kmer_max] CSM_kmer_min: "3" -CSM_kmer_max: "3" +CSM_kmer_max: "5" # options for "pwms" sitecount matrices: # path to the directory with TRANSFAC-formatted PWM files diff --git a/modules/CREATE_SITECOUNT_MATRICES/profiles/local-conda/config.yaml b/modules/CREATE_SITECOUNT_MATRICES/profiles/local-conda/config.yaml index cad0e84..f2acfaa 100644 --- a/modules/CREATE_SITECOUNT_MATRICES/profiles/local-conda/config.yaml +++ b/modules/CREATE_SITECOUNT_MATRICES/profiles/local-conda/config.yaml @@ -1,5 +1,5 @@ snakefile: "../Snakefile" -cores: 64 +cores: 1 printshellcmds: true rerun-incomplete: true use-conda: true