Bio ToolBox
##cancer Cancer related tools
##Fasta.py A lite weighted module for fasta file import and output.
- class Parse(fastaPath) return self.id (list) self.seq (dictionary with key in self.id) self.des (dictionary with key in self.id)
- func write(fadic, savepath, *orderlist=[default []], *description=[default {}])
##grepTsvByCol.py A grep like tool. Could grep a exactly match or not exactly match column in a line.
Usage: grepTsvByCol.py [options]
Options:
-h, --help show this help message and exit
-i INPATH, --input=INPATH
Input file path
-n COLNUM, --columnnum=COLNUM
Column number, start from 1
-t COLTITLE, --columntitle=COLTITLE
Column title
-1, --header Header is true.[Default=False]
-o OUTPATH, --output=OUTPATH
Output file path
-e, --exact Exact match.[Default=False]
Some multithread related tools and examples
Some tools for database collecting and manipulating
This script can sort a matrix either by row or by column, either in or not in reverse order. 1st column and 1st row must be headers.
Usage: sortMatrix.py [options]
Options:
-h, --help show this help message and exit
-i INPATH, --input=INPATH
Input file path
-b, --byrow Sort by row.[Default=False. Default sort by col.]
-r, --reverse Sort in reverse order.[Default=False]
-o OUTPATH, --output=OUTPATH
Output file path
A small tool for soring a table.
The table could have a header line or not, but first column in a line must be a row title. In this version, first column must be row title, and other values in the row must be int or float.
Usage: sortCols.py [options]
Options:
-h, --help show this help message and exit
-i INPATH, --input=INPATH
Input table path
-o OUTPATH, --output=OUTPATH
Output table path
-c COL, --col=COL Sort with col order. If want to sort by multiple
columns, separate items with comma. [Example: 5,3,1]
-r, --reverse Sort in reverse order?
-t, --header Have header line?
A automatic pipeline to run bwa-samtools-sortSam pipeline for either single end or paired end data.
Feature:
- Checkpoint setted during alignment. If any cmd failed because of some reason, just rerun, it would skip finished part.
./bwa-pipe.py -h Usage: bwa-pipe.py [options]
Options:
-h, --help show this help message and exit
-1 FILE1, --read1=FILE1
Read 1 file.
-2 FILE2, --read2=FILE2
Read 2 file. If not given, run bwa in SE mode.
-o PREFIX, --prefix=PREFIX
Output prefix. [Default=bwa_output]
-r REF, --ref=REF Reference fasta path.
-t THREADS, --threads=THREADS
Threads to use. [Default=1]
-g RG, --rg=RG Read Group.
-a OPTION, --option=OPTION
Bwa option. [Default="-e 50 -i 15 -q 10"]
A tools using python, scipy, numpy, matplotlib to make clustered heatmap from a matrix.
Best for Diff exp matrix.