Wildcard Nucleotide Bases

[hyjkim]

I have some pileup data from samtools and it is using wildcards to represent a combination of bases I'm unsure of.

I know the 5 standard bases (ACGTU) and the well known pyrimidine and purine wildcards (YR), but don't know these other wildcards "SMWK". Anyone know what they definitively mean?

Here's some sample pileup output:

NC_000913.2     82      T       W       24      24      60      19     .AAAA.....,,.,...,.     RBBBBBgBhgeBfahdffc
NC_000913.2     3622    A       M       23      23      60      34      .,,C,C.CC,,C,,,.,,,,...g,,.g,,....      ]egBhBaBBhdBhcahdccfBhfBT^[Bb`hhcf
NC_000913.2     6609    G       S       45      45      60      50      .$.,,.C,.,.,C.C,,CC.,..,C,.,.,.,,.,,.,,,.,,,c.c,,^~,^~, a_gh`BhYhZfBBBffBJhXgBdB`gfWYhcBYheBebdfaecBfBhfBB
NC_000913.2     7073    C       Y       21      21      60      40      ,,,.,..,.,,.,,T..,.,.,....,.,,.t.g,ttt.g        ghhhgeQhVhg^ehBee\gBhBhW^hWhVBhBhBBBBBhB
NC_000913.2     1258    G       R       26      26      60      36      ,.,A.,,ACC$,,,C....,,,,,,.,,,,...aat.   h\hB]ghBBBfhfB`cgc_a_a^afhffhdafBBBh
NC_000913.2     3622    A       M       23      23      60      34      .,,C,C.CC,,C,,,.,,,,...g,,.g,,....      ]egBhBaBBhdBhcahdccfBhfBT^[Bb`hhcf
NC_000913.2     13748   T       K       31      31      60      48      .,..,.G,GG,.,...,.,..,.,,......,,,.......,.g,ggg        dgeRhSBhBBhBhfBfhB]abBdOadba\ghWB_ghadchhghBfBBB

[ECO]

IUPAC ambiguity codes...

http://droog.gs.washington.edu/parc/images/iupac.html

S = strong (g/c)
M = aMino (a/c)
W = weak (a/t)
K = keto (g/t)

[hyjkim]

Exactly what I was looking for, thanks very much.

[bi_maniac]

Can anyone tell me how to expand this ambiguity codes with biopython?
I mean, if I call with a sequence like 'YATCG' it returns 2 sequences 'TATCG' and 'CATCG'

Thanks a lot.

[bi_maniac]

I got it. Thank you anyway.

from Bio.Data import IUPACData

#-------------------------------------------
#	Functions
#-------------------------------------------

def expand_wildcards(seq):
	bl = [seq]
	for ix in range(len(seq)):
		sw = True
		while sw:
			iseq = bl.pop(0)
			sl = list(iseq)
			v = IUPACData.ambiguous_dna_values[sl[ix]]
			if len(v) == 1:
				sw = False
				bl.append(iseq)
			else:
				for jx in range(len(v)):
					sl[ix] = v[jx]
					iseq = (''.join(sl))
					bl.append(iseq)

	bl.sort()	# no need indeed
	return bl

[bi_maniac]

^^^^^
It is correctly indented but I do not know how to leave it well. It did not aloow me to upload it as attachment.