A repo for my utilities.
- table_header.py
Just for the boring counting before I do R scripting. Check the columns of the tables.
Options:
-h, --help show this help message and exit
-l LINE_NO, --lines=LINE_NO
header lines to be printed.
-d DIRECTION, --direction=DIRECTION
direction of printing. v or h.
-t TAB_WORD, --tab=TAB_WORD
tab word. s or t. s: space. t: tab.
For example:
./table_head.py annotatePeaks.txt # It is a table generated by HOMER of a ChIP-seq dataset.
col*0 |col*1|col*2|col*3|col*4
PeakID (cmd=/home/....t/TvsC_down_HOMER)|Chr |Start|End |Strand
------------------------------------------------------------------------
col*5 |col*6 |col*7 |col*8
Peak Score|Focus Ratio/Region Size|Annotation|Detailed Annotation
------------------------------------------------------------------------
col*9 |col*10 |col*11 |col*12
Distance to TSS|Nearest PromoterID|Entrez ID|Nearest Unigene
------------------------------------------------------------------------
col*13 |col*14 |col*15 |col*16 |col*17
Nearest Refseq|Nearest Ensembl|Gene Name|Gene Alias|Gene Description
------------------------------------------------------------------------
col*18
Gene Type- intersectSet.py:
A script mimic of bedtools for gene lists.
> ./intersectSet.py --help
usage: intersectSet.py [-h] -a A -b B [-v]
Mimic of bedtools to manipulate gene list set
optional arguments:
-h, --help show this help message and exit
-a A SetA
-b B SetB
-v specific of setA- convertEnsembl2Symbol.R
A script to add a column of gene symbol to correspondent ensembl id.
args[1]: file name, only csv or txt
args[2]: column number of ensembl_id
args[3]: if "1", input file with header; other: no header.