From 6258bfe84ef00b3dc5da68996a014ee03b0060ba Mon Sep 17 00:00:00 2001 From: anastasiia Date: Mon, 14 Jan 2019 12:08:48 +0100 Subject: [PATCH 1/8] rename the parameter for 1.1! min_gap instead of max_bp_between --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index c26cd51..7f3da58 100644 --- a/README.md +++ b/README.md @@ -69,7 +69,7 @@ Optional arguments: --window_length INT This parameter sets the length of a sliding window. (Default: 200) --step INT This parameter sets the number of positions to slide the window forward. (Default: 100) --percentage INT Threshold in percent (Default: 0) - --max_bp_between INT If footprints are less than X bases appart the footprints will be merged (Default: 6) + --min_gap INT If footprints are less than X bases appart the footprints will be merged (Default: 6) Filter motifs: --min_size_fp INT Minimum sequence length threshold. Smaller sequences are discarded. (Default: 10) From d40c91d5ec2f3b39bdd614152b33f8f7116ea75e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ren=C3=A9=20Wiegandt?= Date: Mon, 14 Jan 2019 13:18:13 -0500 Subject: [PATCH 2/8] added gap penalty to glam2; changed footprint extraction parameter --- pipeline.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pipeline.nf b/pipeline.nf index 0ca6c7d..5fc2f21 100644 --- a/pipeline.nf +++ b/pipeline.nf @@ -212,7 +212,7 @@ process footprint_extraction { script: """ - python ${path_bin}/1.1_footprint_extraction/footprints_extraction.py --bigwig ${bigWig} --bed ${bed} --output_file ${name}_called_peaks.bed --window_length ${params.window_length} --step ${params.step} --percentage ${params.percentage} --max_bp_between ${params.max_bp_between} + python ${path_bin}/1.1_footprint_extraction/footprints_extraction.py --bigwig ${bigWig} --bed ${bed} --output_file ${name}_called_peaks.bed --window_length ${params.window_length} --step ${params.step} --percentage ${params.percentage} --min_gap ${params.max_bp_between} """ } @@ -375,7 +375,7 @@ process glam2 { script: """ - glam2 n ${fasta} -O ./${name}/ -a ${params.motif_min_key} -b ${params.motif_max_key} -z 5 -n ${params.iteration} + glam2 n ${fasta} -O ./${name}/ -E 1000 -J 1000 -a ${params.motif_min_key} -b ${params.motif_max_key} -z 5 -n ${params.iteration} """ } @@ -541,7 +541,7 @@ process clustered_glam2 { script: name = fasta.getBaseName() """ - glam2 n ${fasta} -O ./${name}/ -a ${params.motif_min_key} -b ${params.motif_max_key} -z 5 -n ${params.iteration} + glam2 n ${fasta} -O ./${name}/ -E 1000 -J 1000 -a ${params.motif_min_key} -b ${params.motif_max_key} -z 5 -n ${params.iteration} """ } From 14dd70f4637cc56f59df39852d08d2ca221875cb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ren=C3=A9=20Wiegandt?= Date: Mon, 14 Jan 2019 13:20:39 -0500 Subject: [PATCH 3/8] Added gap_penalty parameter --- pipeline.nf | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/pipeline.nf b/pipeline.nf index 5fc2f21..327c278 100644 --- a/pipeline.nf +++ b/pipeline.nf @@ -46,6 +46,7 @@ params.motif_min_key = 8 // Minimum number of key positions (aligned columns) params.motif_max_key = 20 // Maximum number of key positions (aligned columns) params.iteration = 10000 // Number of Iterations done by glam2. A high iteration number equals a more accurate result but with an higher runtime. + params.gap_penalty = 1000 //tomtom params.tomtom_treshold = 0.01 // threshold for similarity score. @@ -57,6 +58,7 @@ params.best_motif = 3 // Top n motifs per cluster + //creating_gtf params.organism="" params.tissue="" @@ -114,6 +116,7 @@ Optional arguments: --iteration INT Number of iterations done by GLAM2. More Iterations: better results, higher runtime. (Default: 10000) --tomtom_treshold FLOAT Threshold for similarity score. (Default: 0.01) --best_motif INT Get the best X motifs per cluster. (Default: 3) + --gap_penalty INT Set penalty for gaps in GLAM2 (Default: 1000) Moitf clustering: --cluster_motif Boolean If 1 pipeline clusters motifs. If its 0 it does not. (Defaul: 0) --edge_weight INT Minimum weight of edges in motif-cluster-graph (Default: 5) @@ -375,7 +378,7 @@ process glam2 { script: """ - glam2 n ${fasta} -O ./${name}/ -E 1000 -J 1000 -a ${params.motif_min_key} -b ${params.motif_max_key} -z 5 -n ${params.iteration} + glam2 n ${fasta} -O ./${name}/ -E params.gap_penalty -J ${params.gap_penalty} -a ${params.motif_min_key} -b ${params.motif_max_key} -z 5 -n ${params.iteration} """ } From 2e6b16935e9315320c1878447710fafd66cc1ed0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ren=C3=A9=20Wiegandt?= Date: Mon, 14 Jan 2019 13:30:49 -0500 Subject: [PATCH 4/8] Added missing brackets --- pipeline.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pipeline.nf b/pipeline.nf index 327c278..251ee7d 100644 --- a/pipeline.nf +++ b/pipeline.nf @@ -378,7 +378,7 @@ process glam2 { script: """ - glam2 n ${fasta} -O ./${name}/ -E params.gap_penalty -J ${params.gap_penalty} -a ${params.motif_min_key} -b ${params.motif_max_key} -z 5 -n ${params.iteration} + glam2 n ${fasta} -O ./${name}/ -E ${params.gap_penalty} -J ${params.gap_penalty} -a ${params.motif_min_key} -b ${params.motif_max_key} -z 5 -n ${params.iteration} """ } @@ -544,7 +544,7 @@ process clustered_glam2 { script: name = fasta.getBaseName() """ - glam2 n ${fasta} -O ./${name}/ -E 1000 -J 1000 -a ${params.motif_min_key} -b ${params.motif_max_key} -z 5 -n ${params.iteration} + glam2 n ${fasta} -O ./${name}/ -E ${params.gap_penalty} -J ${params.gap_penalty} -a ${params.motif_min_key} -b ${params.motif_max_key} -z 5 -n ${params.iteration} """ } From d991ea84c2f5e74d1f305d97a665ba6f206b3b99 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ren=C3=A9=20Wiegandt?= Date: Mon, 14 Jan 2019 13:53:01 -0500 Subject: [PATCH 5/8] pipeline.nf: rename max_bp_between to min_gap --- pipeline.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pipeline.nf b/pipeline.nf index 251ee7d..18a5000 100644 --- a/pipeline.nf +++ b/pipeline.nf @@ -16,7 +16,7 @@ params.window_length = 200 params.step = 100 params.percentage = 0 - params.max_bp_between = 6 + params.min_gap = 6 //filter_unknown_motifs params.min_size_fp=10 @@ -88,7 +88,7 @@ Optional arguments: --window_length INT This parameter sets the length of a sliding window. (Default: 200) --step INT This parameter sets the number of positions to slide the window forward. (Default: 100) --percentage INT Threshold in percent (Default: 0) - --max_bp_between INT If footprints are less than X bases appart the footprints will be merged (Default: 6) + --min_gap INT If footprints are less than X bases appart the footprints will be merged (Default: 6) Filter motifs: --min_size_fp INT Minimum sequence length threshold. Smaller sequences are discarded. (Default: 10) @@ -144,7 +144,7 @@ int_params = ["window_length", "step", "min_size_fp", "max_size_fp", "kmer", "aprox_motif_len", "motif_occurence", "min_seq_length", "global", "sequence_coverage", "memory", "throw_away_seq", "strand", "min_seq", "motif_min_key", "motif_max_key", "iteration", - "edge_weight", "best_motif"] + "edge_weight", "best_motif", "min_gap", "gap_penalty", "edge_weight"] req_params = ["bigwig", "bed", "genome_fasta", "motif_db", "config"] valid_organism = ["hg38", "hg19", "mm9", "mm10"] @@ -215,7 +215,7 @@ process footprint_extraction { script: """ - python ${path_bin}/1.1_footprint_extraction/footprints_extraction.py --bigwig ${bigWig} --bed ${bed} --output_file ${name}_called_peaks.bed --window_length ${params.window_length} --step ${params.step} --percentage ${params.percentage} --min_gap ${params.max_bp_between} + python ${path_bin}/1.1_footprint_extraction/footprints_extraction.py --bigwig ${bigWig} --bed ${bed} --output_file ${name}_called_peaks.bed --window_length ${params.window_length} --step ${params.step} --percentage ${params.percentage} --min_gap ${params.min_gap} """ } From 85ffa449468762097381937068a52df2e4e6f676 Mon Sep 17 00:00:00 2001 From: renewiegandt Date: Mon, 14 Jan 2019 20:15:11 +0100 Subject: [PATCH 6/8] Fixed typo in README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 7f3da58..be16aba 100644 --- a/README.md +++ b/README.md @@ -69,7 +69,7 @@ Optional arguments: --window_length INT This parameter sets the length of a sliding window. (Default: 200) --step INT This parameter sets the number of positions to slide the window forward. (Default: 100) --percentage INT Threshold in percent (Default: 0) - --min_gap INT If footprints are less than X bases appart the footprints will be merged (Default: 6) + --min_gap INT If footprints are less than X bases apart the footprints will be merged (Default: 6) Filter motifs: --min_size_fp INT Minimum sequence length threshold. Smaller sequences are discarded. (Default: 10) From 5987297b7484781a9a19b9349f3bbe4499f8446f Mon Sep 17 00:00:00 2001 From: renewiegandt Date: Mon, 14 Jan 2019 20:15:53 +0100 Subject: [PATCH 7/8] Removed newline in pipeline.nf --- pipeline.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/pipeline.nf b/pipeline.nf index 18a5000..bc7415c 100644 --- a/pipeline.nf +++ b/pipeline.nf @@ -58,7 +58,6 @@ params.best_motif = 3 // Top n motifs per cluster - //creating_gtf params.organism="" params.tissue="" From 4dc537f6e9bd018380fb4695f4fbdf83973839bc Mon Sep 17 00:00:00 2001 From: renewiegandt Date: Mon, 14 Jan 2019 20:16:24 +0100 Subject: [PATCH 8/8] Fixed typo in pipeline.nf --- pipeline.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipeline.nf b/pipeline.nf index bc7415c..dcab67a 100644 --- a/pipeline.nf +++ b/pipeline.nf @@ -87,7 +87,7 @@ Optional arguments: --window_length INT This parameter sets the length of a sliding window. (Default: 200) --step INT This parameter sets the number of positions to slide the window forward. (Default: 100) --percentage INT Threshold in percent (Default: 0) - --min_gap INT If footprints are less than X bases appart the footprints will be merged (Default: 6) + --min_gap INT If footprints are less than X bases apart the footprints will be merged (Default: 6) Filter motifs: --min_size_fp INT Minimum sequence length threshold. Smaller sequences are discarded. (Default: 10)