p300 support

.gitignore

@@ -6,6 +6,7 @@
 **/ananse/
 anansenake.egg-info/
 build/
+config.yaml
 dask-worker-space/
 example/config.yaml
 example/outdir/

CHANGELOG.md

@@ -19,6 +19,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ### Added
 
+- experimental p300 support
 - run differential gene expression analysis using `DESeq2` from `Seq2Science` RNA-seq output
 - run peak enrichment analysis using `gimmemotifs maelstrom` from `Seq2Science` ATAC-seq output
 - obtain nonhuman transcription factor binding motifs using `gimmemotifs motif2factors`

anansnake/envs/ananse.yaml

@@ -5,3 +5,7 @@ channels:
  - defaults
 dependencies:
  - ananse =0.5.0
+
+ - pip
+ - pip:
+ - git+https://github.com/vanheeringen-lab/ANANSE.git@p300_2

anansnake/envs/gimme.yaml

@@ -8,3 +8,7 @@ dependencies:
  - gffread
  - orthofinder
  - xgboost # optional maelstrom dependency
+
+ - pip
+ - pip:
+ - git+https://github.com/vanheeringen-lab/gimmemotifs@report

anansnake/rules/ananse.smk

@@ -18,6 +18,7 @@ rule binding:
  expand("{benchmark_dir}/binding_{{condition}}.txt", **config)[0]
  params:
  atac_samples=lambda wildcards: CONDITIONS[wildcards.condition]["ATAC-seq samples"],
+ enhancer_data=lambda wildcards: "-P" if config.get("enhancer_data") == "p300" else "-A",
  jaccard=config["jaccard"],
  threads: 1 # multithreading not required when using a pfmscorefile
  resources:
@@ -35,7 +36,7 @@ rule binding:
  printf "using columns: {params.atac_samples}\n\n" > {log}
 
  ananse binding \
- -A {input.atac} \
+ {params.enhancer_data} {input.atac} \
  -c {params.atac_samples} \
  -g {input.genome} \
  -p {input.pfm} \

example/config.yaml

@@ -50,6 +50,7 @@ merged_technical_reps: true # set to false if you used 'technical_replicates: "
 merged_biological_reps: true # set to false if you used 'biological_replicates: "keep" in s2s'
 
 # ANANSE binding
+enhancer_data: ATAC # experimental option: p300
 jaccard: 0.2 # default: 0.1
 
 # ANANSE influence

requirements.yaml

@@ -4,4 +4,4 @@ channels:
  - bioconda
  - defaults
 dependencies:
- - seq2science =1.2.0
+ - seq2science =1.2.1