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  • Wildcard Nucleotide Bases

    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:
    Code:
    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

  • #2
    IUPAC ambiguity codes...



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

    Comment


    • #3
      Exactly what I was looking for, thanks very much.

      Comment


      • #4
        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.

        Comment


        • #5
          I got it. Thank you anyway.

          Code:
          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
          Last edited by GenoMax; 11-15-2015, 01:34 PM. Reason: Added CODE tags

          Comment


          • #6
            ^^^^^
            It is correctly indented but I do not know how to leave it well. It did not aloow me to upload it as attachment.

            Comment

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