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pyGetGeneNamesFromGTF (version 1.0.0)

Choose GTF File from:

GTF File --gtf:

GTF file containing gene ID co-ordinates

Select the attribute to extract names from --attribute:

Count occurences of each annotation --count:

Enter output file label -o:

pyGetGeneNamesFromGTF

pyGetGeneNamesFromGTF is part of the pyCRAC package. Extracts and counts all gene names from a GTF file.

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.
-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
--count
                      with this flag you the program will count the
                      occurence for each source/annotation in the gtf file