diff --git a/.gitignore b/.gitignore index 6d3ce93..eba22ea 100644 --- a/.gitignore +++ b/.gitignore @@ -6,6 +6,7 @@ **/ananse/ anansenake.egg-info/ build/ +config.yaml dask-worker-space/ example/config.yaml example/outdir/ diff --git a/CHANGELOG.md b/CHANGELOG.md index 64013d5..a4c8d3c 100644 --- a/CHANGELOG.md +++ b/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` diff --git a/anansnake/envs/ananse.yaml b/anansnake/envs/ananse.yaml index 63e9a6b..33242fc 100644 --- a/anansnake/envs/ananse.yaml +++ b/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 diff --git a/anansnake/envs/gimme.yaml b/anansnake/envs/gimme.yaml index 455a5db..3e01953 100644 --- a/anansnake/envs/gimme.yaml +++ b/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 diff --git a/anansnake/rules/ananse.smk b/anansnake/rules/ananse.smk index ce4a170..410d0c8 100644 --- a/anansnake/rules/ananse.smk +++ b/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} \ diff --git a/example/config.yaml b/example/config.yaml index 69c5c99..19d2f3a 100644 --- a/example/config.yaml +++ b/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 diff --git a/requirements.yaml b/requirements.yaml index 2147e05..0df8ddd 100644 --- a/requirements.yaml +++ b/requirements.yaml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - seq2science =1.2.0 + - seq2science =1.2.1