illegal blast configurations allowed to be submitted about tripal_blast

[ekcannon]

Compatible and proper default parameters for all 4 programs are in pull request #33.

[laceysanderson]

Good catch! A PR would be greatly appreciated :-)

[bradfordcondon]

ill have one tomorrow am, i want to read the manual and make sure i catch all the invalid combinations.

[bradfordcondon]

The reward/penalty in the manual for blastn lists the below reward/penalty and gap open/extend costs.

I can't find a similar table for the other blast methods, are they the same?

Anyway, the table has me wonder, what is the logic behind the available gap/mismatch options? I ask because if one chooses 4 -5 for matching, then the only valid gap options are 6/5, 5/5, 4/5, 3/5 (or more stringent), none of which are options.

reward/penalty	gap costs (open/extend)	default MegaBLAST gap costs (open/extend)
1/-5	3/3	0/5.5
1/-4	1/2, 0/2, 2/1, 1/1	0/4.5
2/-7	2/4, 0/4, 4/2, 2/2	0/8
1/-3	2/2, 1/2, 0/2, 2/1, 1/1	0/3.5
2/-5	2/4, 0/4, 4/2, 2/2	0/6
1/-2	2/2, 1/2, 0/2, 3/1, 2/1, 1/1	0/2.5
2/-3	4/4, 2/4, 0/4, 3/3, 6/2, 5/2, 4/2, 2/2	0/4
3/-4	6/3, 5/3, 4/3, 6/2, 5/2, 4/2	N/A
4/-5	6/5, 5/5, 4/5, 3/5	N/A
1/-1	3/2, 2/2, 1/2, 0/2, 4/1, 3/1, 2/1	N/A
3/-2	5/5	N/A
5/-4	10/6, 8/6	N/A

[ekcannon]

@bradfordcondon, the advanced options were implemented by a student with limited understanding of how blastn and friends actually work. Although we spent some time working together to ensure that it was not possible to select invalid combinations of settings, due to lack of time, the effort was unfortunately, minimal. I wouldn't take too seriously any of the existing decisions about which options are available under which conditions.

Unfortunately, the options are not the same for each BLAST program. One source of information, if there is no handy table, is to check available options in the NCBI BLAST interface. (https://blast.ncbi.nlm.nih.gov/Blast.cgi)

[bradfordcondon]

Shoot, thank you @ekcannon very good to know that the valid choices are d ifferent for each.

I made a table below for the valid/invald combinations for blastn.

I wonder if switching it to free text instead of the dropdown would be the best solution, if different combinations are going to be valid/invalid for each program? Otherwise I can make this matrix for each program and add the validation for each, but that might take me a little while to get around to.

blasn

reward penalty value			gap open extend
	5,2	2,2	1,2	0,2	3,1	2,1	1,1
1,-1	yes	yes	yes	yes	yes	yes	no
1,-2	yes	yes	yes	yes	yes	yes	yes
1,-3	yes	yes		yes	yes	yes	yes
1,-4	yes	yes	yes	yes	yes	yes	yes
4,-5	no	no	no	no	no	no	no
2,-3	yes	yes	no	no	yes	no	no

edit my main concern is blast failing without a good error message passed to the user. This came up because a user selected a 4,-5 blastn and got an ambiguous "job failed" message.

also good suggestion just going by the options available in web blast, ill do that

I'd bet thats what your student did, but they only looked at the default options. The gap cost options change depending on the selected match/mismatch.

[ekcannon]

Illegal blastn combinations removed by @bradfordcondon (pull request #32).

blastp, blastx, and tblastx remain.

[laceysanderson]

Fixed by PRs!