viola.Bedpe.rename_info

Bedpe.rename_info(table_name, value, safety_mode=True)

Rename INFO name of this object.

Parameters

• table_name (str) – Current table name.

• value (str) – A New table name.

• safety_mode (bool) – Protect against potentially destructive renaming.

Return type

None

Examples

>>> import viola
>>> from io import StringIO
>>> DATA = """chrom1    start1  end1    chrom2  start2  end2    name    score   strand1 strand2 test1   test2
    chr1        10      11      chr1    20      21      test1   60      +       -       True    1
    chr2        10      11      chr2    20      21      test2   60      -       +       False   23
    chr2        10      11      chr2    40      41      test3   60      +       +       True    32
    chr3        10      11      chr4    20      21      test4   60      -       -       True    13
"""
>>> bedpe = viola.read_bedpe(StringIO(DATA), patient_name="patient1")
>>> print(bedpe)
INFO=svlen,svtype,cipos,ciend,test1,test2
Documentation of Bedpe object ==> https://dermasugita.github.io/ViolaDocs/docs/html/reference/bedpe.html
      id      be1      be2 strand  qual svtype
0  test1  chr1:11  chr1:21     +-    60    DEL
1  test2  chr2:11  chr2:21     -+    60    DUP
2  test3  chr2:11  chr2:41     ++    60    INV
3  test4  chr3:11  chr4:21     --    60    BND
>>> bedpe.rename_info('test1', 'renamed')
INFO=svlen,svtype,cipos,ciend,renamed,test2
Documentation of Bedpe object ==> https://dermasugita.github.io/ViolaDocs/docs/html/reference/bedpe.html
      id      be1      be2 strand  qual svtype
0  test1  chr1:11  chr1:21     +-    60    DEL
1  test2  chr2:11  chr2:21     -+    60    DUP
2  test3  chr2:11  chr2:41     ++    60    INV
3  test4  chr3:11  chr4:21     --    60    BND