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"Klebsiella_grimontii_strain_4928STDY7071328_chromosome_1_NZ_LR607336": { + "genome_gc": 3017473, + "genome_length": 6099119, + "cds_gc": 2752380, + "number_of_genes": 4974 + }, + "Sinorhizobium_medicae_strain_USDA1037_NZ_VITA01000068": { + "cds_gc": 3525250, + "number_of_genes": 6240, + "genome_gc": 3996619, + "genome_length": 6534206 + }, + "Vibrio_cyclitrophicus_strain_ECSMB14105_chromosome_1_NZ_CP039701": { + "genome_gc": 2221124, + "genome_length": 5074401, + "cds_gc": 1919241, + "number_of_genes": 4319 + }, + "Brevundimonas_diminuta_strain_NCTC8545_NZ_UIGE01000001": { + "genome_gc": 2312944, + "genome_length": 3438815, + "cds_gc": 2112818, + "number_of_genes": 3376 + }, + "Pseudomonas_parafulva_strain_PRS09_11288_NZ_CP019952": { + "genome_gc": 2894710, + "genome_length": 4690783, + "cds_gc": 2600299, + "number_of_genes": 4134 + }, + "ALL_Moraxella_catarrhalis_strain_CCRI_195ME_NZ_CP018059": { + "cds_gc": 736105, + "number_of_genes": 1837, + "genome_gc": 828892, + "genome_length": 1994386 + }, + "ALL_Deinococcus_radiodurans_strain_R1_dM1_chromosome_I_NZ_CP031501": { + "genome_gc": 2188402, + "genome_length": 3283189, + "cds_gc": 1977247, + "number_of_genes": 3148 + }, + "Brucella_abortus_strain_BFY_chromosome_1_NZ_CP007737": { + "cds_gc": 1680303, + "number_of_genes": 3164, + "genome_gc": 1881293, + "genome_length": 3288158 + }, + "Halomonas_alkalicola_strain_M2_NZ_CP130143": { + "genome_gc": 2721527, + "genome_length": 3989759, + "cds_gc": 2482739, + "number_of_genes": 3650 + } +} \ No newline at end of file diff --git a/src/marbel/data_generations.py b/src/marbel/data_generations.py index 745a306..bc519fd 100644 --- a/src/marbel/data_generations.py +++ b/src/marbel/data_generations.py @@ -14,7 +14,7 @@ from iss.app import generate_reads as gen_reads from marbel.presets import AVAILABLE_SPECIES, model, pm, pg_overview, species_tree, PATH_TO_GROUND_GENES_INDEX, DGE_LOG_2_CUTOFF_VALUE -from marbel.presets import DEFAULT_PHRED_QUALITY, ErrorModel, LibrarySizeDistribution, __version__ +from marbel.presets import DEFAULT_PHRED_QUALITY, ErrorModel, LibrarySizeDistribution, __version__, species_stats_dict def draw_random_species(number_of_species): @@ -397,6 +397,12 @@ def generate_report(summary_dir, gene_summary): species_subtree = species_tree.copy() species_subtree.prune(gene_summary["origin_species"].unique().tolist()) f.write(species_subtree.write()) + species = gene_summary["origin_species"].unique().tolist() + species_subset = {k: v for k, v in species_stats_dict.items() if k in species} + species_info_df = pd.DataFrame.from_dict(species_subset, orient="index") + num_sampled_genes = gene_summary.groupby("origin_species").size() + species_info_df["num_sampled_genes"] = num_sampled_genes + species_info_df.to_csv(f"{summary_dir}/species_stats.csv") def create_sample_values(gene_summary_df, number_of_samples, first_group, a0, a1): diff --git a/src/marbel/presets.py b/src/marbel/presets.py index aef3553..f174228 100644 --- a/src/marbel/presets.py +++ b/src/marbel/presets.py @@ -3,6 +3,7 @@ from importlib import resources from ete3 import Tree from enum import Enum +import json __version__ = "0.1.3" @@ -39,10 +40,12 @@ PATH_TO_GROUND_GENES_INDEX = f"{data_package}/deduplicated_pangenome_EDGAR_Microbiome_JLAB2.fas.bgz.bio_index" PANGENOME_OVERVIEW = f"{data_package}/orthologues_processed_combined_all.parquet" SPECIES_PHYLO_TREE = f"{data_package}/EDGAR_all_species.newick" +SPECIES_STATS = f"{data_package}/species_stats.json" pg_overview = pd.read_parquet(PANGENOME_OVERVIEW, engine='pyarrow') species_tree = Tree(SPECIES_PHYLO_TREE) DGE_LOG_2_CUTOFF_VALUE = 1 +species_stats_dict = json.load(open(SPECIES_STATS, 'r')) AVAILABLE_SPECIES = pg_overview.columns.to_list()[:MAX_SPECIES]