def test_geneprof(): g = GeneProf(verbose=False) #res = g.get_list_experiments(with_outputs=True) res = g.get_list_experiments(with_outputs=False) len(res) > 0 res = g.get_metadata_experiment("3") g.get_metadata_experiment(Id="385", with_workflow=True) g.get_metadata_dataset("11_12_122_1", with_ats=True)
def test_geneprof(): g = GeneProf(verbose=False) #res = g.get_list_experiments(with_outputs=True) res = g.get_list_experiments(with_outputs=False) len(res)>0 res = g.get_metadata_experiment("3") g.get_metadata_experiment(Id="385", with_workflow=True) g.get_metadata_dataset("11_12_122_1", with_ats=True)
def test_get_tfas(): g = GeneProf(verbose=False) g.get_tfas_by_gene("mouse", "9885") g.get_tfas_by_gene("human", "36958", frmt="xml", include_unbound=True) g.get_tfas_by_gene("mouse", "14899", frmt="txt", ats="C_NAME,C_ENSG") g.get_tfas_by_gene("human", "36958", frmt="rdata") g.get_tfas_by_sample("mouse", 541) g.get_tfas_by_sample("human", "784", frmt="xml", include_unbound=True) g.get_tfas_by_sample("mouse", "541", frmt="txt", ats="C_NAME,C_ENSG") g.get_tfas_by_sample("human", "784")
def test_gettargets(): g = GeneProf(verbose=False) g.get_targets_tf("mouse", "9885") g.get_targets_tf("human", "36958", include_unbound=True) g.get_targets_tf("mouse", "14899", ats="C_NAME,C_ENSG") g.get_targets_tf("human", "36958", frmt="rdata") g.get_targets_by_experiment_sample("mouse", "541") g.get_targets_by_experiment_sample("human", "784", include_unbound=True) g.get_targets_by_experiment_sample("mouse", "541", ats="C_NAME,C_ENSG") g.get_targets_by_experiment_sample("human", "784", frmt="rdata")
def test_3(): g = GeneProf(verbose=False) g.get_gene_id("mouse", "C_ENSG", "ENSMUSG00000059552") g.get_gene_id("human", "C_RSEQ", "NM_005657") g.get_gene_id("human", "any", "NM_005657") g.get_external_gene_id("mouse", "715", "C_ENSG") g.get_external_gene_id("mouse", "2981", "C_RSEQ") g.get_external_gene_id("mouse", "2981", "C_NAME") g.get_list_idtypes("mouse") g.get_list_idtypes("human") g.get_gene_expression("mouse", "715", with_sample_info=True) g.get_gene_expression("mouse", "715", output="RAW") g.get_gene_expression("mouse", "715", frmt="txt", with_sample_info=True) g.get_gene_expression("mouse", "715", frmt="rdata", with_sample_info=True)
def test_2(): g = GeneProf(verbose=False) g.search_experiments("sox2") g.search_experiments("citation:cancer") g.search_experiments("citation:'stem cell'") g.search_datasets('sox2') g.search_datasets('gene expression') g.search_datasets("datatype:GENOMIC_REGIONS AND sox2") g.search_samples("ChIP") g.search_samples("Gene:sox2") g.search_samples("human")
def test_1(): g = GeneProf(verbose=False) g.get_list_reference_datasets() g.get_list_experiment_samples("mouse") g.get_list_experiment_samples("human", frmt="txt") g.get_list_experiment_samples("human", frmt="rdata") g.search_genes("sox2") g.search_genes("sox2", taxons="9606") g.search_genes("sox2", taxons="9606, 10090") res = g.search_genes("brca2 AND cancer AND reference", taxons="mouse")
def test_get_tf(): g = GeneProf(verbose=False) g.get_tf_by_target_gene("mouse", "715", with_sample_info=True) g.get_tf_by_target_gene("mouse", "715", frmt="xml", with_sample_info=True) g.get_tf_by_target_gene("mouse", "715", frmt="txt") g.get_tf_by_target_gene("mouse", "715", frmt="rdata", with_sample_info=True) g.get_tfas_scores_by_target("mouse", "715", with_sample_info=True) g.get_tfas_scores_by_target("mouse", 715, with_sample_info=True) g.get_tfas_scores_by_target("mouse", 715, frmt="txt") g.get_tfas_scores_by_target("mouse", "715", frmt="rdata", with_sample_info=True)
def test_3(): g = GeneProf(verbose=False) g.get_gene_id("mouse", "C_ENSG", "ENSMUSG00000059552") g.get_gene_id("human", "C_RSEQ", "NM_005657") g.get_gene_id("human", "any", "NM_005657") g.get_external_gene_id("mouse","715", "C_ENSG") g.get_external_gene_id("mouse","2981", "C_RSEQ") g.get_external_gene_id("mouse","2981", "C_NAME") g.get_list_idtypes("mouse") g.get_list_idtypes("human") g.get_gene_expression("mouse", "715", with_sample_info=True) g.get_gene_expression("mouse", "715", output="RAW") g.get_gene_expression("mouse", "715", frmt="txt", with_sample_info=True) g.get_gene_expression("mouse", "715", frmt="rdata", with_sample_info=True)
def test_data(): g = GeneProf(verbose=False) g.get_data("11_119_18_1", frmt="txt", gz=True) g.get_data( "11_119_18_1", frmt="txt", gz=True, ats= "C_ENSG,C_11_119_16_1_RPKM0,C_11_119_16_1_RPKM1,C_11_119_16_1_RPKM2,C_11_119_16_1_RPKM3" ) g.get_chromosome_names("pub_mm_ens58_ncbim37", frmt="txt") g.get_chromosome_names("pub_hs_ens59_grch37", frmt="json") g.get_chromosome_names("11_3_7_2", frmt="xml") g.get_bed_files("11_3_7_2") g.get_bed_files("11_3_7_2", chromosome="3-chr3") g.get_bed_files("zebrafish", with_track_description=False) g.get_bed_files("11_12_125_2", filter_column="C_11_12_125_2_14_TFBS") g.get_wig_files("11_58_16_2") g.get_wig_files("11_12_112_2", with_track_description=False, only_distinct=True, frag_length=200) g.get_fasta("11_385_6_1") g.get_fastq("11_385_6_1")
def geneprof(): return GeneProf(verbose=False)
def test_data(): g = GeneProf(verbose=False) g.get_data("11_119_18_1", frmt="txt", gz=True) g.get_data("11_119_18_1", frmt="txt", gz=True, ats="C_ENSG,C_11_119_16_1_RPKM0,C_11_119_16_1_RPKM1,C_11_119_16_1_RPKM2,C_11_119_16_1_RPKM3") g.get_chromosome_names("pub_mm_ens58_ncbim37", frmt="txt") g.get_chromosome_names("pub_hs_ens59_grch37", frmt="json") g.get_chromosome_names("11_3_7_2", frmt="xml") g.get_bed_files("11_3_7_2") g.get_bed_files("11_3_7_2", chromosome="3-chr3") g.get_bed_files("zebrafish", with_track_description=False) g.get_bed_files("11_12_125_2", filter_column="C_11_12_125_2_14_TFBS") g.get_wig_files("11_58_16_2") g.get_wig_files("11_12_112_2", with_track_description=False, only_distinct=True, frag_length=200) g.get_fasta("11_385_6_1") g.get_fastq("11_385_6_1")