bgsignature 0.2

Command line interface

The 3 tools can be called using

• bgsignature count

• bgsignature frequency

• bgsignature normalize

Some examples:

• getting help:

  bgsignature -h
  bgsignature frequency -h

• count triplets in mutation that fall in certain regions using hg38:

  bgsignature count -m my/muts/file -r my/regions/file
  -g hg38 -o my/output.json --cores 4

Python

Alternative, the command line options have an equivalent in Python:

from bgsignature import count, relative_frequency, normalize

that accept similar parameters except the output. The return object can be used as a dictionary.

If you already have your files loaded in Python you can use directly count function in the corresponding module. E.g.:

from bgsignature.count import mutation
mutation.count(mutations, 'hg38', 3)

In addition, you can also use the the “low-level” functions that do the count (count_all and count_group) which are much simple and do not perform any kind of parallelization. E.g.:

from bgsignature.count import mutation
mutation.count_all(mutations, 'hg38', 3)
# or to group mutations by sample
mutation.count_group(mutations, 'hg38', 3, 'SAMPLE')

The return object can be normalized to 1, using the sum1() method or divided by some normalization counts using the normalize() method.

Mutations file

Tab separated file (can be compressed into gz, bgz or xz formats) with a header and at least these columns: CHROMOSOME, POSITION, REF, ALT. In addition, SAMPLE, CANCER_TYPE and SIGNATURE are optional columns that can be used for grouping the signature.

Regions file

Tab separated file (can be compressed into gz, bgz or xz formats) with a header and at least these columns: CHROMOSOME, START, END, ELEMENT. In addition, SYMBOL, and SEGMENT are optional columns that can be used for grouping the signature.