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pyExtractLinesFromGTF (version 1.0.0)

Choose GTF File from:

GTF File --gtf:

GTF file containing gene ID co-ordinates

File containing gene list --genes_file:

Tabular file with 1 column of gene or annotation names

Select the attribute to extract names from --attribute:

Extract lines from GTF that -v:

Enter output file label -o:

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