Remove ambiguous bases from alignment sequence

Question

[a.moner]

Hi, could you please help me with this I have very big alignment file and there are many ambiguous bases,

1- I want to replace them (Y, W, S, R, M and K) with ( _ )

2- remove the entire column that includes this ambiguity and keep just the four bases A, T, C, G and remove all gaps

thanks here an example

S1 CCGCCGCCGCCTCC

S2 CCGCCGCCGWCTCC

S3 CCGCCMCCGCCTCC

S4 CCGCCTCCGCCTCC

I want the output for the first question like this

S1 CCGCCGCCGCCTCC

S2 CCGCCGCCG_CTCC

S3 CCGCC_CCGCCTCC

S4 CCGCCTCCGCCTCC

I want the output for the second question like this

S1 CCGCCCCGCTCC

S2 CCGCCCCGCTCC

S3 CCGCCCCGCTCC

S4 CCGCCCCGCTCC

[microfuge]

t_coffee provides very good alignment reformatting options here. For example to change all A to 1 and T to a gap

t_coffee -other_pg seq_reformat -in=input.aln -output=clustalw_aln -out=output.aln -action  +convert 'A1' 'T-'

The command for removing gapped columns is here

t_coffee -other_pg seq_reformat -in=a.aln -output=clustalw_aln -out=test.aln -action  +convert +rm_gap  n

n after rm_gap has to be set accordingly.