hyacinlee / genomeScript

Short Script of genome analysis

genomeScript

gapFinder.py

find gap in genome fasta

telBlock.py

creat Telomere in chromsome start and end

splitScaf.py

split scaf and chromsome Fasta to contig by remove N

mergeSV.sh

bash commond to merge sv result of smartie and sniff

formatTable.py

usage: formatTable.py [-h] [-b] [-f] [-ft] [--bc [...]] [--fc [...]] [--exc]

RunCmd : Funciton: use a table split file to handle fasta && table files Writer : Minghui Meng [e-mail]

1) Extract or Except saome line by mutiple-col number 
    ./formatTable.py -b bait.table -f fish.table
    ./formatTable.py -b bait.table -f fish.table --bc 1,2  --fc 2,3 --except  

optional arguments: -h, --help show this help message and exit -b table split bait file (default: None) -f fish file (default: None) -ft type of fish file (default: table) --bc [ ...] set bait file columns,suppose like 1,2,3 (default: [1]) --fc [ ...] set fish file columns,suppose like 2,3,4 (default: [1]) --exc except bait lines (default: False)