Gene_analysis

The script is used for

1. Gene query: Find genes associated with disease or phenotype from OMIM, ClinVar, Orphanet, and HPO database
2. Gene name normalization: Normalize gene name from multiple database
3. Gene depth analysis: Calculate the precentage of gene regions that base coverage < depth

Requirements

sambamba (gene depth analysis)
pandas
numpy

Gene query

usage: gene_query.py [-h] --keyword KEYWORD --output OUTPUT

optional arguments:
  -h, --help            show this help message and exit
  --keyword KEYWORD, -k KEYWORD
                        keyword to query in database. e.g. "Kennedy disease"
  --output OUTPUT, -o OUTPUT
                        output directory

Note

• Latest OMIM data should be acquired from the website (https://www.omim.org/downloads) OMIM database (2021/07) in database

Output

• detail_<keyword>.xls: detail gene information from all database
• genelist_<keyword>.txt: total gene from all database

Gene name normalization

usage: gene_check.py [-h] --genelist GENELIST --output OUTPUT

optional arguments:
  -h, --help            show this help message and exit
  --genelist GENELIST, -g GENELIST
                        genlist file path for analysis. Gene with new line "\n" splitted.
  --output OUTPUT, -o OUTPUT
                        output directory

Output

• <genelist_basename>_checked.txt: final gene list. filter-out gene will be in the beginning of the file

Gene depth analysis

usage: gene_depth.py [-h] [--depth DEPTH] --output OUTPUT --genelist GENELIST
                     [--bamlist BAMLIST] --dir_bed DIR_BED --mapping_quality
                     {MQ0,MQ10,MQ20,MQ30} [{MQ0,MQ10,MQ20,MQ30} ...]

optional arguments:
  -h, --help            show this help message and exit
  --depth DEPTH, -d DEPTH
                        base depth for analysis. default:20
  --output OUTPUT, -o OUTPUT
                        output directory
  --genelist GENELIST   gene list file. Delimiter "\n"
  --bamlist BAMLIST     bam list file
  --dir_bed DIR_BED, -b DIR_BED
                        directory where bed files locate. bed file name should be <gene>.bed
  --mapping_quality {MQ0,MQ10,MQ20,MQ30} [{MQ0,MQ10,MQ20,MQ30} ...]

Output

• <output>_<mapping_quality>.xls