pySelectMotifsFromGTF

pySelectMotifsFromGTF is part of the pyCRAC package. Extracts your favourite k-mer sequence from pyMotif GTF output files. Note that you can include degenerate nucleotides in your motif string:

N = A, G, C or T
R = A or G = puRine
Y = C or T = pYrimidine
M = A or C = aroMatic
S = G or C
W = A or T
K = G or T = Keto
V = A, C or G = Not T (letter after)
D = A, G or T = Not C
H = A, C or T = Not G
B = C, G or T = Not A

So if you enter KBCTTG as search string and length=6, then the program will extract a large number of six-mers from your data. If you set length = 8, it will look for this pattern in a stretch of 8 nucleotides.

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 FILE, --output=FILE
                    Optional.Specify the name of the output file. Default
                    is standard output. Make sure it has the .gtf
                    extension!
-m KBCTTG, --motif=KBCTTG
                    Specify the motif you want extract from the GTF file.
-z 15.0, --Z_score=15.0
                    Set a minimum k-mer Z-score. Default=0
-l 4, --length=4
                    Set a k-mer length. Default is no length filtering