mafStats

5 July 2012

Author

Dent Earl

Description

A program to read MAF file and report back statistics about the contents.

Installation

1. Download the package.
2. cd into the directory.
3. Type make.

Use

mafStats --maf mafFile.maf [options]

Options

• -h, --help show this help message and exit.
• -m, --maf path to maf file.

Example

$ mafStats --maf smallDemo.maf
smallDemo.maf
------------------------------
File size:       66.13 MB
Lines:             212986
Header lines:           5
s lines:           144592
e lines:                0
i lines:                0
q lines:                0
Blank lines:        68388
Comment lines:          1
Sequence chars:     49181016 ( 77.65%)
Gap chars:          14154166 ( 22.35%)
Blocks:                      34194
Ave block area:            1852.23
Max block area:              37840
Ave seq field length:       340.14
Max seq field length:         7568
Ave seq count in block:       4.23
Max seq count in block:          5
10 unique sequences, ordered by # bases present:
            simHuman.chr1:      5311230 ( 10.80%)
            simHuman.chr0:      5225141 ( 10.62%)
              simDog.chr1:      5048843 ( 10.27%)
              simDog.chr0:      5023883 ( 10.22%)
              simCow.chr1:      4989381 ( 10.14%)
              simCow.chr0:      4979544 ( 10.12%)
            simMouse.chr1:      4671434 (  9.50%)
            simMouse.chr0:      4654920 (  9.46%)
              simRat.chr1:      4654607 (  9.46%)
              simRat.chr0:      4622033 (  9.40%)
                    total:     49181016 (100.00%)