def load(file: str): return SampleDataArray.parse(json.loads(Utilities.load_string(file)))
from vradchenko.lactobacillus_salivarius.ProjectDescriber import ProjectDescriber INDEX_COL_NAME = "sample_name" SAMPLE_NAMES = ("1sq_FTP", "2sq_FTP", "336g_Nextera", "517_Nextera") # LOGS_DIR_ROOT = os.path.join(ProjectDescriber.ROOT_DIR, "pga-pe", "log") # TOOL_NAMES = ("fastqc", "trimmomatic", "cutadapt", "remove_hg", "bowtie2") TOOL_VERSIONS = dict( fastqc_version="quay.io/biocontainers/fastqc:0.11.8--1", trimmomatic_version="quay.io/biocontainers/trimmomatic:0.39--1", cutadapt_version="quay.io/biocontainers/cutadapt:2.5--py37h516909a_0", bowtie2_version="quay.io/biocontainers/bowtie2:2.3.5--py37he860b03_0", spades_version="quay.io/biocontainers/spades:3.9.1--0") templates_dir = os.path.join(ProjectDescriber.ROOT_DIR, "reports", "1") template = jinja2.Template( Utilities.load_string(os.path.join(templates_dir, "template.txt"))) for sample_name in SAMPLE_NAMES: # sample_name = SAMPLE_NAMES[0] # combined_assembly_statistics_df = Utilities.load_tsv( os.path.join(".", ProjectDescriber.OWNER, ProjectDescriber.NAME, "data", "tables", "combined_assembly_statistics.tsv")) submission_report_df = Utilities.load_tsv( os.path.join(".", ProjectDescriber.OWNER, ProjectDescriber.NAME, "data", "tables", "ncbi", "submission_report.tsv")) # submission_combined_df = pd.concat([ i.set_index(INDEX_COL_NAME) for i in (combined_assembly_statistics_df, submission_report_df) ],