btb

Bio ToolBox

##cancer Cancer related tools

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##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 {}])

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##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]

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multithread

Some multithread related tools and examples

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refDB

Some tools for database collecting and manipulating

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sortMatrix.py

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

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sortCols.py

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?

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bwa-pipe.py

version 1.0

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"]

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heatmap.cluster.plot.py

A tools using python, scipy, numpy, matplotlib to make clustered heatmap from a matrix.

Best for Diff exp matrix.