seqits 0.0.2

Tools for sequences process

Seqits

Seqits provides several useful toosl for sequences processing.

Installation method

pip install seqits

Tools

Seqits

python -m seqits -v # display the version of Seqits
python -m seqits list # display all tools in Seqits

randseq

This tool can generate cds or protein sequence(s) randamly.

Arguments	Description
type	nucl/prot, cds or protein sequence(s)
num	number of sequences(s) to generate
out (optional)	output file, defaut: output.fa
show(optional)	whether display the output on the screen or not, defaut: false

e.g.
python -m seqits.randseq nucl 100 -o output.fa -s true

search

This tool can search and extract sequence(s) you want by Gene ID or Gene Name.

Arguments	Description
input	input raw fasta file
gene	input gene(s)
type (optional)	re/string/file, type of input gene(s). re means regulate expression, for file, one gene one line; for string, gene(s) should be seperated with ',', default string
mode (optional)	fast/order, "fast" mode may faster than "order" mode, but "order" mode can display your output accoring to the order of input gene(s), default: fast
out (optional)	output file, defaut: output.fa
show (optional)	whether display output on the screen or not, defaut: false

e.g.
python -m seqits.search input.fa Gene1,Gene2,Gene3 --out output.fa
python -m seqits.search input.fa Gene.txt -t file

formatseq

This tool can format the fasta file.

Arguments	Description
input	input raw fasta file
num (optional)	number of characters per line, defaut: 60
out (optional)	output file, defaut: output.fa
show (optional)	whether display output on the screen or not, defaut: false

e.g.
python -m seqits.formatseq input.fa 100

retest

This tool can test the regulate expression.

Arguments	Description
input	input file
re	regulate expression

e.g.
python -m seqits.retest input.fa ">(Gene\d{1,3})"