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)
],
