def script__datadump_whats_my_species(folder, sample):
folder = str(folder)
sample = str(sample)
data_dict = datahandling.load_sample_component(sample)
data_dict["summary"] = data_dict.get("summary", {})
data_dict["results"] = data_dict.get("results", {})
data_dict = datahandling.datadump_template(
data_dict, folder, "log/setup__filter_reads_with_bbduk.err.log",
extract_bbuk_log)
data_dict = datahandling.datadump_template(data_dict, folder,
"bracken.txt",
extract_bracken_txt)
data_dict = datahandling.datadump_template(
data_dict, folder, "kraken_report_bracken.txt",
extract_kraken_report_bracken_txt)
data_dict = datahandling.datadump_template(data_dict, folder,
"kraken_report.txt",
extract_kraken_report_txt)
data_dict = combine_bbduk_log_bracken_txt_kraken_report_bracken_txt(
data_dict)
datahandling.save_sample_component(data_dict, sample)
return 0
def script__datadump_assemblatron(folder, sample):
folder = str(folder)
sample = str(sample)
data_dict = datahandling.load_sample_component(sample)
data_dict["summary"] = data_dict.get("summary", {})
data_dict["results"] = data_dict.get("results", {})
data_dict = datahandling.datadump_template(data_dict, folder,
"contigs.sum.cov",
extract_contigs_sum_cov)
data_dict = datahandling.datadump_template(data_dict, folder,
"contigs.bin.cov",
extract_contigs_bin_cov)
data_dict = datahandling.datadump_template(
data_dict, folder, "log/setup__filter_reads_with_bbduk.err.log",
extract_bbuk_log)
data_dict = datahandling.datadump_template(data_dict, folder,
"quast/report.tsv",
extract_quast_report)
data_dict = datahandling.datadump_template(data_dict, folder,
"contigs.variants",
extract_contig_variants)
data_dict = datahandling.datadump_template(data_dict, folder,
"contigs.stats",
extract_contig_stats)
data_dict = datahandling.datadump_template(data_dict, folder,
"contigs.sketch",
extract_contig_sketch)
datahandling.save_sample_component(data_dict, sample)
return 0
def script__datadump_whats_my_species(folder, sample):
folder = str(folder)
sample = str(sample)
data_dict = datahandling.load_sample_component(sample)
data_dict["summary"] = data_dict.get("summary", {})
data_dict["results"] = data_dict.get("results", {})
data_dict = datahandling.datadump_template(data_dict, folder,
"bracken.txt",
extract_bracken_txt)
data_dict = datahandling.datadump_template(
data_dict, folder, "kraken_report_bracken.txt",
extract_kraken_report_bracken_txt)
data_dict = datahandling.datadump_template(data_dict, folder,
"kraken_report.txt",
extract_kraken_report_txt)
data_dict = species_math(data_dict)
datahandling.save_sample_component(data_dict, sample)
return 0
def script__datadump_min_read_check(folder, sample):
folder = str(folder)
sample = str(sample)
data_dict = datahandling.load_sample_component(sample)
data_dict["summary"] = data_dict.get("summary", {})
data_dict["results"] = data_dict.get("results", {})
data_dict = datahandling.datadump_template(
data_dict, folder, "log/setup__filter_reads_with_bbduk.err.log",
extract_bbuk_log)
datahandling.save_sample_component(data_dict, sample)
return 0