Extract gene expression data which matches to custom gene list.
It is python codes and use "python gene_list_extractor.py -i input_gene_file -l gene_list_file (-o output_file -c1 1 -c2 1)" to run!
Example of input_gene_file is provided as gene_expression_data.txt.
sample1 sample2 sample3 sample4 sample5
geneA 1 3 5.5 7 2
geneB 100 267 55 79 62
geneC 0.3 0.65 9.5 0.87 2.1
geneD 205 356 78 67 2900
geneE 1001 3001 5500 7001 2001
geneF 2 2 2 2 2
geneG 0.01 0.03 0.5 0.07 0.02
Example of gene_list_file is provided as gene_list.txt.
geneA
geneG
geneI
geneP
geneW
geneX
gene_list_extractor.py requires -i input_gene_file -l gene_list_file. Those parameters are optional; -o output_file -c1 column_number_of_gene_id_in_input_gene_file -c2 column_number_of_gene_id_in_gene_list_file.
-h, --help show this help message and exit
-i INPUT, --input INPUT input gene expression file name
-l LIST, --list LIST input gene list file name
-o OUTPUT, --output OUTPUT output file name
-c1 COLUMN_INPUT, --column_input COLUMN_INPUT default 1; column number in gene ID location in input gene expression file
-c2 COLUMN_LIST, --column_list COLUMN_LIST default 1; column number in gene ID location in gene list file
Example of output_file is provided as gene_data.txt.
geneA 1 3 5.5 7 2
geneG 0.01 0.03 0.5 0.07 0.02
geneI 8 9 5 7 4
geneP 6.5 3.5 5.5 9.5 11.5
geneW 190 23 9.6 790 2.4
geneX 290 3.6 565.5 7.5 280