promoter

promoter_design/FANTOM_CAT.lv3_robust.tss.sortedby_fantomcage.hg38.v4.tsv

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promoter_design/Homo_sapiens.GRCh38.dna.primary_assembly.fa

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promoter_design/Homo_sapiens.GRCh38.dna.primary_assembly.fa.fai

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promoter_design/Homo_sapiens.GRCh38.dna.primary_assembly.fa.mmap

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promoter_design/README.md

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+## FANTOM Input Data 
+
+#### Input Signal
+agg.plus.bw.bedgraph.bw
+agg.minus.bw.bedgraph.bw
+
+Please unzip bigwig files before using the data.
+
+#### Blacklist Regionts for hg38
+fantom.blacklist8.plus.bed.gz
+fantom.blacklist8.plus.bed.gz.tbi
+fantom.blacklist8.minus.bed.gz
+fantom.blacklist8.minus.bed.gz.tbi
+
+#### Sorted TSS 
+FANTOM_CAT.lv3_robust.tss.sortedby_fantomcage.hg38.v4.tsv
+
+best.sei.model.pth.tar
+target.sei.names
+
+#### Human Reference genome used for analysis
+Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz 
+
+Please unzip human reference before using it.
+
+#### Python script file
+Promoter design script requires one-hot represenation of human genome. 
+make_genome_memmap.py script creates .mmap file. See instruction of files 
+how  to run it. 

promoter_design/agg.minus.bw.bedgraph.bw

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promoter_design/agg.plus.bw.bedgraph.bw

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promoter_design/best.sei.model.pth.tar

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promoter_design/fantom.blacklist8.minus.bed.gz

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promoter_design/fantom.blacklist8.minus.bed.gz.tbi

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promoter_design/fantom.blacklist8.plus.bed.gz

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promoter_design/fantom.blacklist8.plus.bed.gz.tbi

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promoter_design/make_genome_memmap.py

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+"""
+This script converts the genome fasta file to a memory map
+file of genome one-hot encodings. This is used to accelerate
+genome sequence retrieval.
+
+Example usage: python make_genome_memmap.py
+"""
+
+import sys
+sys.path.append("/data/xsu2/dirichlet-flow-matching")
+
+import pathlib
+from utils.selene_utils import MemmapGenome
+
+
+if __name__ == "__main__":
+    hg38 = MemmapGenome(
+        input_path="Homo_sapiens.GRCh38.dna.primary_assembly.fa",
+        memmapfile="Homo_sapiens.GRCh38.dna.primary_assembly.fa.mmap",
+        init_unpicklable=True,
+    )