Feature request - MAAPS (Mixed Amino Acid Position Screening) tool

[InaMBerry]

I will probably be starting on a new Dengue project this fall and I would need some help with a script for the sequence data I will be using. Basically, I need to screen many Miseq sequences for occurrence of mixed amino acid positions.

Current tools for sequence analyses allow for export of a consensus sequence with mixed nucleotide positions, that is, when both A and G are found in a certain position that position is designated as R. However, when the sequence is translated into amino acids, and A in this position encodes say Gly while G encodes Pro, the exported amino acid consensus sequence will just have a ? for this mixed amino acid position. I would need a script that:

1. Goes through the sequence and designates the mixed amino acid positions as Gly/Pro instead (that is, informs of the exact amino acid composition of this position)
2. Counts how many mixed amino acid positions that are found in a sequence
3. Provides me with the exact position number of the mixed positions
4. Preferably provides information on what gene these mixed positions are found in

For this I will be providing Dengue full genome miseq nucleotide consensus sequences (using standard IUPAC codes for mixed nucleotide positions). Start will be the first Met of the coding region. Since Denv1,2,3 and 4 genes differ slightly in their positions on the genome, this will need to be taken into account for 4.

Thanks!

[necrolyte2]

@demis001 Please work with @InaMBerry on this portion of bio_pieces

It will be a great introduction on how to work with travis-ci.org, readthedocs.org, coveralls.io

[demis001]

@InaMBerry

Can you share sample data inputs and a template output you expected (some sort of table with header)? It would be nice if the inputs are from the real data.

[averagehat]

It occurred to me that while the only examples we discussed were codons with one ambiguous base, it is also possible (correct me if I'm wrong) for a codon to have 2 or 3 ambiguous bases, i.e. ARR or RRR

[InaMBerry]

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That is true and we need to account for that as well.

-----Original Message-----
From: averagehat [mailto:[email protected]]
Sent: Friday, May 22, 2015 3:19 PM
To: VDBWRAIR/bio_pieces
Cc: Maljkovic Berry, Irina CTR USARMY MEDCOM WRAIR (US)
Subject: Re: [bio_pieces] Feature request - MAAPS (Mixed Amino Acid Position Screening) tool (#22)

It occurred to me that while the only examples we discussed were codons with one ambiguous base, it is also possible (correct me if I'm wrong) for a codon to have 2 or 3 ambiguous bases, i.e. ARR or RRR

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