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initiate_infrastructure_example.py
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"""
"""
import sys
sys.path.insert(0, '/home/kai/KEMALINECIK/from_raf_computer/Kemal/RiboSeqAnalysis')
from infrastructure.main import *
temp_repo_dir = "/home/kai/KEMALINECIK/from_raf_computer/Kemal/Temp/human"
data_repo_dir = "/home/kai/KEMALINECIK/from_raf_computer/Kemal/Data/sam_bukau"
script_path_infrastructure = "/home/kai/KEMALINECIK/from_raf_computer/Kemal/RiboSeqAnalysis/infrastructure"
spt = [os.path.join(data_repo_dir, i) for i in ["Sixtymers_TT1.sam", "Sixtymers_TT2.sam"]]
sps = [os.path.join(data_repo_dir, i) for i in ["Sixtymers_Rep1.sam", "Sixtymers_Rep2.sam", "Sixtymers_NoPK.sam"]]
erb_serb = [os.path.join(data_repo_dir, f"SeRP/EBP1/Rep{i+1}/IP/IP{i+1}.sam") for i in range(2)]
erb_total = [os.path.join(data_repo_dir, f"SeRP/EBP1/Rep{i+1}/Total/Total{i+1}.sam") for i in range(2)]
nac_serb = [os.path.join(data_repo_dir, f"SeRP/NAC/Rep{i+1}/IP/IP{i+1}.sam") for i in range(2)]
nac_total = [os.path.join(data_repo_dir, f"SeRP/NAC/Rep{i+1}/Total/Total{i+1}.sam") for i in range(2)]
coco_d = [os.path.join(data_repo_dir, i) for i in ["Coco_Dis1.sam", "Coco_Dis2.sam"]]
coco_m = [os.path.join(data_repo_dir, i) for i in ["Coco_Mono1.sam", "Coco_Mono2.sam"]]
exclude_genes = ["ENSG00000160789"]
I = Infrastructre(temp_repo_dir,
exclude_genes=exclude_genes,
ensembl_release=102,
organism="homo_sapiens",
#include_gene3d=True,
verbose=True)
# Should be first to calculate, since multiprocessing is quite memory inefficient.
I.riboseq_coco = RiboSeqCoco(I.temp_repo_dir, coco_m, coco_d, "cocoassembly",
riboseq_assign_to="best_transcript", riboseq_assign_at=-15,
protein_genome_instance=I.protein_genome,
gene_info_dictionary=I.gene_info,
exclude_genes=I.exclude_genes, verbose=I.verbose)
I.riboseq_sixtymers = RiboSeqSixtymers(I.temp_repo_dir, spt, sps, "sixtymers",
riboseq_assign_to="best_transcript", riboseq_assign_at="auto",
protein_genome_instance=I.protein_genome,
gene_info_dictionary=I.gene_info,
exclude_genes=I.exclude_genes, verbose=I.verbose)
# I.riboseq_selErb = RiboSeqSelective(I.temp_repo_dir, erb_total, erb_serb, "selectiveErb",
# riboseq_assign_to="best_transcript", riboseq_assign_at="auto",
# protein_genome_instance=I.protein_genome,
# gene_info_dictionary=I.gene_info,
# exclude_genes=I.exclude_genes, verbose=I.verbose)
#
# I.riboseq_selNac = RiboSeqSelective(I.temp_repo_dir, nac_total, nac_serb, "selectiveErb",
# riboseq_assign_to="best_transcript", riboseq_assign_at="auto",
# protein_genome_instance=I.protein_genome,
# gene_info_dictionary=I.gene_info,
# exclude_genes=I.exclude_genes, verbose=I.verbose)