8 Other Ultilities

8.1 findCCGG

  • Command
cgmaptools findCCGG -h
#   Usage: cgmaptools findCCGG -i <genome.fa> [-o <output>]
#         (aka FiindCCGG)
#   Description: Get the positions of all the C'CGG---CCG'G fragments.
#   Contact:     Guo, Weilong; guoweilong@126.com
#   Last Update: 2018-01-02
#   Output Ex:
#       chr1    4025    5652
#       chr1    8274    8431
#   
#   Options:
#     -h, --help  show this help message and exit
#     -i FILE     Genome sequence file in Fasta format
#     -o FILE     Name of the output file (standard output if not specified).
#                 Format: chr cCgg_pos ccGg_pos (0-base)

  • Example

    cgmaptools findCCGG -i genome.fa -o genome.ccgg

8.2 bed2fragreg

  • Command
cgmaptools bed2fragreg -h
#   Usage: cgmaptools bed2fragreg [-i <BED>] [-n <N>] [-F <50,50,..> -T <50,..>] [-o output]
#         (aka FragRegFromBED)
#   Description: Generate fragmented regions from BED file.
#   Contact:     Guo, Weilong; guoweilong@126.com
#   Last Update: 2018-05-02
#      Split input region into N bins, get fragments from 5' end and 3' end.
#   Input Ex:
#      chr1   1000    2000   +
#      chr2   9000    8000   -
#   Output Ex:
#      chr1   +   940  950  1000 1200 1400 1600 1800 1850
#      chr2   -   9060 9050 9000 8800 8600 8400 8200 8150
#   
#   
#   Options:
#     -h, --help   show this help message and exit
#     -i FILE      BED format, STDIN if omitted
#     -F INT_list  List of region lengths in upstream of 5' end, Ex: 10,50. List
#                  is from 5'end->3'end
#     -T INT_list  List of region lengths in downstream of 3' end, Ex: 40,20. List
#                  is from 5'end->3'end
#     -n INT       Number of bins to be equally split [Default:1]
#     -o OUTFILE   To standard output if omitted. Compressed output if end with
#                  .gz

  • Example

  • Output format

    • Example
    chr1   +   940  950  1000 1200 1400 1600 1800 2000 2060 2080
chr2   -   9060 9050 9000 8800 8600 8400 8200 8000 7960 7940
    • Column Description
Output format description for cgmaptools bed2fragreg

Figure 8.1: Output format description for cgmaptools bed2fragreg

[POS_1, POS_2), [POS_2, POS_3), … [POS_(n-1), POS_n) will be used as input for cgmaptools mfg