malacology/TNT_Script
1
0
Fork 0
Code Issues Pull requests Projects Releases 12 Wiki Activity

add: fasta input func

Browse source
This commit is contained in:
kuoi 2023-10-10 17:17:29 +08:00
parent 957a4a9400
commit a23c2f3335
1 changed files with 24 additions and 2 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

26
guoyi.run
View file

@ -15,6 +15,8 @@ if ( (argnumber == 0) || (argnumber >7) )
| === Parameters Details === | | === Parameters Details === |
| ============================== | | ============================== |
| filename type weight K cons resamp prefix | | filename type weight K cons resamp prefix |
| - filename extension must be lower case |
| fas/fasta tnt/ss are allowed |
| - type should be 32, dna, prot, num | | - type should be 32, dna, prot, num |
| num=number, dna=DNA, prot=protein | | num=number, dna=DNA, prot=protein |
| 32=max number allowed (default) | | 32=max number allowed (default) |
@ -44,16 +46,31 @@ var:
dostr domjr dohlf contype dostr domjr dohlf contype
doew doiw doeiw dowt wtstring wttype doew doiw doeiw dowt wtstring wttype
kvalue kvalue
search; search
isfas istnt input;
set dojak 0; set doboot 0; set dosym 0; set dobrs 0; set dorbrs 0; set rsmp 0; set dobremer 0; set dojak 0; set doboot 0; set dosym 0; set dobrs 0; set dorbrs 0; set rsmp 0; set dobremer 0;
set dostr 0; set domjr 0; set dohlf 0; set dostr 0; set domjr 0; set dohlf 0;
set doew 0; set doiw 0; set doeiw 0; set dowt 0; set wttype 0; set doew 0; set doiw 0; set doeiw 0; set dowt 0; set wttype 0;
set kvalue 12; set kvalue 12;
set search 0; set search 0;
set isfas 0; set istnt 0;
goto=%0; goto=%0;
/*Get prefix and extension of input*/
set input $%1;
/*confirm input format*/
if ((eqstring [ $input>. fas ]) || (eqstring [ $input>. fasta ]))
set isfas 1;
else
if ((eqstring [ $input>. tnt ]) || (eqstring [ $input>. ss ]))
set istnt 1;
else
errmsg extension name of input file must be fas/fasta (for fas format) or tnt/ss (for Hennig86/NONA/TNT format);
end end
/*handle weighting type*/ /*handle weighting type*/
if (argnumber>=3) if (argnumber>=3)
set wtstring $%3; set wtstring $%3;
@ -185,7 +202,12 @@ if ('dowt')
end end
/*Reopen tnt*/ /*Reopen tnt*/
procedure %1; if ('istnt')
procedure $input;
else
if ('isfas')
procedure & $input;
end end
hold 10000; hold 10000;
/*handle search*/ /*handle search*/