YXK_Usefull_Tools

Dependence

python-docx

jieba

numpy

scipy

met_brewer

Pandas

A simple Python package and some simple scripts for the beginner of Bioinformatics.

faSpliter.py

faSpliter.py is a script in order to split your fasta file into multiple pieces.

ReverseComplement.py

ReverseComplement.py is a script to reverse part of your sequence by reversing complementary sequences.

getGFFLEN.py

getGFFLEN.py is a small script for building the GFF and LEN files required for WGDI

usage:

python3 getGFFLEN.py [gff] [whether you want mRNA or gene: mRNA/gene/CDS, anything matches your fastaID] [the abbreviation of your species] [cds.path] [pep.path]

sbatch.py

sbatch.py also is a simple script for sbatch system job submission, srun mode and straight submission mode are supported.   

srun mode is only can be executed in one line

1.

echo {YOUR CMD} >> cmd.txt  

2.

python3 ./sbatch.py -s cmd.txt -n {YOUR JOBS NAME} -p {NODENAMES} -c 1 -t 1 -srun(yes or no REQUIRED) -y (yes or [EMPTY] OPTIONAL)  

diploidGffRenamder.py is a simple script for organizing your gff3 file

python ./Gff3Renamer.py <GFF3: STR/PATH> <ABBREVIATION: STR> <CONTIGMARKER: STR> <PEP: STR> <CDS: STR> <GENE: STR>  

plinkSNP2fasta.py

plinkSNP2fasta.py extracts SNPs information from VCF and chromosomes fasta, generating multiple chromosomes fasta files based on your sample numbers.

python3 plinkSNP2fasta.py <CHR_FASTA> <SNP_VCF> <OUTDIR>  

parablast.sh

parablast.sh is a simple script that runs blast in parallel mod

bash parablast.sh reference_genome(dir) query_genome(dir) data_type(pep/dna str) parts(int) threads(int)  

Requirements are:

ParaFly,

ncbi-blast

and

split_FA.pl (Which is from TangerZhang, you can find this script in YXK_Usefull_Tools)

faRC.py

A simple script for DNA sequences reverse and complement

python3 faRC.py <DNA.fa: STR> <seqName: STR || IdList.txt: STR || 0: INT>

Instructions: 
	<seqName>		This is an ID, if you want only one sequence get reversed and complemented
	<IdList.txt>	This is a file containing all of the id you want to reverse and complement
	<0>				Means reverse and complement all of your fasta files.