averagehat / haskell-maaps Goto Github PK

https://github.com/VDBWRAIR/Haskell-MAAPs/blob/master/src/Lib.hs#L112-L114

i is used instead of the calculated ntIndex variable.

This is non-obvious and should be in the doc, and functionality covered by a test

To get a full idea of the ambiguity content within a sequence it's more accurate to also include those ambiguities that do not result in an amino acid change and label them as synonymous, otherwise when investigators compare the output to manually curated output I envision it will be initially confusing.

Rather than make it a native function perhaps just adding an option for the investigator to record all ambiguities. So the default can be mixed amino acid positions only but if the investigator wants synonymous too perhaps they can add the flag '--syn true' or just --syn

We want to pull out the PAC (integer list of ALT percentages) from the INFO column as well as the ALT column (character list of the ALT bases). Also include the DP. This needs to be done for every nucleotide in the codon, which makes the output tricky.

Right now the output looks like:

ID	Codon	NTPos  	AA  AAPos	 RowType   
2055	RAC	 1927 	N/D  643	Non_Synonymous

Maybe add the following columns:

Nt1                Nt2             Nt3       Nt1DP     Nt2DP      Nt3DP
A=28,G=62,T=10    A=90,C=5,G=5    C=99,A=1     990        100        360

NtXDP could be placed into the NtX columns instead of having the extra columns for DP.

Thoughts?

Please clarify in the README how many characters are allowed in the sequence identifier to 'show up' in the output. I had 4 conditions all beginning with "Q4":

Q4_1_NexteraRawCons
Q4_1_KAPARawCons
Q4_6_NexteraRawCons
Q4_6_KAPARawCons

The output -

ID      Codon   NTPos   AA      AAPos   RowType

Q4      RAA     1444    K/E     482     Non_Synonymous
Q4      TWC     1676    Y/F     559     Non_Synonymous
Q4      ARC     4025    N/S     1342    Non_Synonymous
Q4      GAW     5991    E/D     1997    Non_Synonymous

Q4      RAA     1444    K/E     482     Non_Synonymous
Q4      TWC     1676    Y/F     559     Non_Synonymous
Q4      RCC     5620    T/A     1874    Non_Synonymous

Q4      RAA     1444    K/E     482     Non_Synonymous
Q4      TWC     1676    Y/F     559     Non_Synonymous

Q4      RAA     1444    K/E     482     Non_Synonymous
Q4      TWC     1676    Y/F     559     Non_Synonymous
Q4      RTR     7939,7941       I/M/V   2647    Non_Synonymous

As you can see I don't know which conditions is which as the identifiers were cut off. So it would be helpful to know how many characters I am allowed or that an underscore won't work in identifier names etc...