pyExtractLinesFromGTF
pyExtractLinesFromGTF is part of the pyCRAC package. Extracts lines from a GTF file that contain gene names of interest.
Parameter list
Options:
--gtf=Yourfavoritegtf.gtf type the path to the gtf file that you want to use. By default it expects data from the standard input. -g FILE, --genes_file=FILE name of your gene list or annotations list file (1 column) -o OUTFILE, --outfile=OUTFILE type the name and path of the file you want to write the output to. Default is standard output -a ATTRIBUTE, --attribute=ATTRIBUTE from which attribute do you want to extract names? Choices: gene_name, gene_id, transcript_name, transcript_id -v similar to grep -v option. Remove the genes from the GTF that are in the gene list