I have one fasta file which has 30 sequences and pattern file which contain different motifs.
I need to match my motifs with fasta sequences and location in which it is authenticated should be highlight like this :
The script which I have developed until now :
# biopython from Bio import SeqIO # regex library import re # file with FASTA sequence infile = r"C:UsersLenovoDesktopfnlpythPromoter Sequence.fasta" # pattern to search for iupac = 'GGCA' # look through each FASTA sequence in the file for seq_record in SeqIO.parse(infile, "fasta"): print ("Sequence ID: ", seq_record.id, "; ", len(seq_record), "bp") print (seq_record.seq) print(iupac) # scan for IUPAC; re.I makes search case-insensitive matches = re.findall( iupac, str(seq_record.seq), re.I) if matches: print ("Matches = ", len(matches))
I need help to complete this script?