Gene Information

##Introduction

Code in this repository was used to generate GeneInfomation.txt which contain infomation as follows:

chrN
start_codon
end_codon
symbol_of_chain: + or -
transcript_number
gene_id gene_name gene_biotype
te_in_gene: gene_length overlapped_TE_length TE_fraction_in_this_gene
te_in_cds: cds_length_of_this_gene cds_length_overlapped_TE TE_fraction_in_cds
disease_gene: -(not in OMIM) year(added in OMIM in 1996)

Each line above stands for a column (seperated by '\t') in the output file, GeneInfomation.txt

##Run program

To generate GeneInfo.txt, all you need to do is 3 simple steps.

1, clone GeneInfo project to your Linux environment.

git clone https://github.com/danfengcao/GeneInfo.git


2, Download gene annotation **ensembl.gtf** and repeat annotation **human19.rm**.
>```
cd GeneInfo/data
wget ftp://ftp.ensembl.org/pub/release-73/gtf/homo_sapiens/Homo_sapiens.GRCh37.73.gtf.gz
wget http://www.repeatmasker.org/genomes/hg19/RepeatMasker-rm405-db20140131/hg19.fa.out.gz
gunzip -c Homo_sapiens.GRCh37.73.gtf.gz > ensembl.gtf
gunzip -c hg19.fa.out.gz > human19.rm

3, Run the program and you will get the result in GeneInfomation.txt

cd .. python GeneInfo.py data/ensembl.gtf data/human19.rm data/newDiseaseGeneEachYear


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If you have any question or suggestion, please send email to me(danfengcao.info@gmail.com).

如果您有任何疑问或建议，欢迎发邮件给我（danfengcao.info@gmail.com）。