samples = [s.mate for s in samples_pyro] cluster = illumitag.clustering.Cluster(samples, 'soda_model_lakes') # Upload raw samples for SRA # pool = illumitag.runs[3][7] pool.create_raw_samples() for s in samples: s.sra.upload_to_sra() for s in samples_pyro: s.sra.upload_to_sra() # Create BioSamples # from illumitag.helper.sra import MakeSpreadsheet make_tsv = MakeSpreadsheet(cluster) make_tsv.write_bio_tsv() # Submit to SRA # make_tsv.write_sra_tsv() # The pyro samples # cluster_pyro = illumitag.clustering.Cluster(samples_pyro, 'soda_model_lakes_pyro') make_tsv_pyro = MakeSpreadsheet(cluster_pyro) make_tsv_pyro.platform = "LS454" make_tsv_pyro.instrument_model = "454 GS FLX Titanium" make_tsv_pyro.forward_read_length = "500" make_tsv_pyro.reverse_read_length = "500" make_tsv_pyro.forward_filetype = "sff" make_tsv_pyro.reverse_filetype = "sff" make_tsv_pyro.write_sra_tsv() # Copy files #cp /My\ Folders/PHD/Server/Uppmax_home/ILLUMITAG/views/clusters/soda_model_lakes_pyro/sra/sra_submission.tsv /My\ Folders/PHD/-ILLUMITAQ-/Other/SRA\ spreadsheet/soda/2.tsv #cp /My\ Folders/PHD/Server/Uppmax_home/ILLUMITAG/views/clusters/soda_model_lakes/sra/sra_submission.tsv /My\ Folders/PHD/-ILLUMITAQ-/Other/SRA\ spreadsheet/soda/1.tsv
