Ejemplos de GeneProf.get_chromosome_names en Python

Ejemplo n.º 1

Archivo: test_geneprof.py Proyecto: schryer/bioservices

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")

Ejemplo n.º 2

Archivo: test_geneprof.py Proyecto: cxhernandez/bioservices

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")