Python script for motif analysis for Cserhati, 2019
This script is run on a whole genome sequence, and calculates the score for all possible motifs of length n, ordered in lexicographic order. Since there are four bases, there are 4n possible motifs. The score of any given motif is S = (O - E)/(O + E), where O is the observed occurrence of a given motif, and E is its expected occurrence based on the base pair background distribution, which is also determined by the script. S then takes a value between -1 and 1 for under-represented and over-represented motifs, respectively.
The script is run the following way:
python motif_analysis.py -i <inputfile> -o <outputfile> -s <species name> -n <motif length>
where the flags mean the following things:
-i : the input whole genome sequence in fasta format.
-o : the output statistics file with the number of contigs, the bp distribution, and the motif sequence, the observed and expected occurrences as well as the score value.
-s : the species name
-n : the motif length (usually between 5 and 12 bp)
A sample of the output file is as follows:
#Species No. chr. Genome length A% C% G% T%
#GCF_002217835.1_Dobs_1.0_genomic.fna 1935 181868570 0.278804967467 0.221933285975 0.222036923996 0.277224822562
#Motif Observed Expected Score
AAAAAAA 257119 23815.5822242 0.83045460594
AAAAAAC 57298 18957.5905639 0.502788177924
AAAAAAG 51056 18966.4433466 0.458275306026
AAAAAAT 88520 23680.6058956 0.577888092376
AAAAACA 63707 18957.5905639 0.541337096463
AAAAACC 29016 15090.5502374 0.315722941096
AAAAACG 23060 15097.5971964 0.208671493717