from collections import defaultdict

file_paths = defaultdict(dict)
# P. stutzeri RCH2
file_paths['rch2']['name'] = 'P. stutzeri RCH2'
file_paths['rch2']['bowtie_lib'] = '/mnt/data2/DAP-seq/libs/rch2/rch2'
file_paths['rch2']['size'] = 4600000
file_paths['rch2']['fitgenomics_file'] = '/mnt/data2/DAP-seq/scripts/dap-seq-utils/dap-seq-utils/data/rch2/fitgenomics.tsv'
file_paths['rch2']['operons_file'] = '/mnt/data2/DAP-seq/scripts/dap-seq-utils/dap-seq-utils/data/rch2/operons2.tsv'
file_paths['rch2']['utrs_file'] = '/mnt/data2/DAP-seq/scripts/dap-seq-utils/dap-seq-utils/data/rch2/rch2_utrs75.tsv'
file_paths['rch2']['replicons_file'] = '/mnt/data2/DAP-seq/scripts/dap-seq-utils/dap-seq-utils/data/rch2/replicons.tsv'
file_paths['rch2']['sequence_file'] = '/mnt/data2/DAP-seq/scripts/dap-seq-utils/dap-seq-utils/data/rch2/rch2.fna'
# P. fluorescens N2E2
file_paths['n2e2']['name'] = 'P. fluorescens N2E2'
file_paths['n2e2']['bowtie_lib'] = '/mnt/data2/DAP-seq/libs/n2e2/n2e2'
file_paths['n2e2']['size'] = 6900000
file_paths['n2e2']['fitgenomics_file'] = '/mnt/data2/DAP-seq/scripts/dap-seq-utils/dap-seq-utils/data/n2e2/n2e2_genes.tsv'
file_paths['n2e2']['operons_file'] = '/mnt/data2/DAP-seq/scripts/dap-seq-utils/dap-seq-utils/data/n2e2/operons3.tsv'
file_paths['n2e2']['utrs_file'] = '/mnt/data2/DAP-seq/scripts/dap-seq-utils/dap-seq-utils/data/n2e2/n2e2_utrs75.tsv'
file_paths['n2e2']['replicons_file'] = '/mnt/data2/DAP-seq/scripts/dap-seq-utils/dap-seq-utils/data/n2e2/replicons.tsv'
file_paths['n2e2']['sequence_file'] = '/mnt/data2/DAP-seq/scripts/dap-seq-utils/dap-seq-utils/data/n2e2/n2e2.fna'
# P. putida KT2440
file_paths['kt2440']['name'] = 'P. putida KT2440'
file_paths['kt2440']['bowtie_lib'] = '/mnt/data2/DAP-seq/libs/kt2440/kt2440'
file_paths['kt2440']['size'] = 6200000
file_paths['kt2440']['fitgenomics_file'] = '/mnt/data2/DAP-seq/scripts/dap-seq-utils/dap-seq-utils/data/kt2440/fitgenomics.tsv'
file_paths['kt2440']['operons_file'] = '/mnt/data2/DAP-seq/scripts/dap-seq-utils/dap-seq-utils/data/kt2440/operons2.tsv'
file_paths['kt2440']['utrs_file'] = '/mnt/data2/DAP-seq/scripts/dap-seq-utils/dap-seq-utils/data/kt2440/kt2440_utrs75.tsv'
file_paths['kt2440']['replicons_file'] = '/mnt/data2/DAP-seq/scripts/dap-seq-utils/dap-seq-utils/data/kt2440/replicons.tsv'
file_paths['kt2440']['sequence_file'] = '/mnt/data2/DAP-seq/scripts/dap-seq-utils/dap-seq-utils/data/kt2440/kt2440.fna'
