trimal -selectcols doesn't work

[inab]

trimal -selectcols doesn't work

[scapella]

Hi, Could you please indicate the command-line used? Thanks! S El dom., 16 feb. 2020 19:25, darap888 <[email protected]> escribió:

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ERROR: Parameter "-selectcols" not valid. I found somewhere pdf manual, where "select" is used instead - still the same error — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#56>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAA7RB7JSSYMHTP7RDZLIQLRDGALPANCNFSM4KWFRDTA> .

[darap888]

Thank you for response.

I tried several variations because I was not sure, how to use it

trimal -in t1.fas -out t2.fas -select {0-592,4268-5581}

and

trimal -in t1.fas -out t2.fas -selectcols {0-592,4268-5581}

and without gap after option

trimal -in t1.fas -out t2.fas -selectcols{0-592,4268-5581}

and with a gap after bracket

trimal -in t1.fas -out t2.fas -selectcols { 0-592,4268-5581}

and without brackets at all

trimal -in t1.fas -out t2.fas -selectcols 0-592,4268-5581

When I use option -noallgaps, it is working perfectly

Thnx in advance.

[scapella]

Could you please try out? trimal -in t1.fas -out t2.fas -selectcols { 0-592,4268-5581 }

As parsing arguments from command-line in C++ is difficult, we decided that the best way to do it is by asking for the opening bracket "{", blank space, all individual columns and/or intervals together separated either by "," and/or "-"; then blank space, and the closing bracket "}"

Hope it helps,

S

[darap888]

Actually, I tried it in the first place. It did not work.
In the end, I trimmed these columns with mothur pcr.seqs, as my colleague suggested (in case, anyone would need this function).

Anyway, I used trimal to delete all-gaps columns and it was good for my purpose.

Thank you very much again.

[camilogarciabotero]

Hi @scapella,

I am also struggling with the -selectcols option. I've tried some of the variations with the "{}" symbols with space, without space, etc. However, when using it as the best way suggested e.g. -selectcols { 0-2142,0-2142 } (here I want to delete the first 2142 columns of my alignment), the problem continues. I could spot an error from my terminal (I'm using z-shell on OS X Catalina).

I'm still stuck on this issue. So, if you can give me some lights on how to overcome it, I would really appreciate this.

Regards,
Camilo.

[nicodr97]

Hi @camilogarciabotero,

It seems that this is an issue with zsh parsing curly braces. You can either change to bash in your terminal or you can add a slash or single quotes to curly braces.
Option 1: exec bash to change current shell and use the following arguments -selectcols { 0-2142,0-2142 }
Option 2: execute it with zsh and the following arguments -selectcols \{ 0-2142,0-2142 \} or -selectcols '{' 0-2142,0-2142 '}'

As for what @darap888 commented,
Are you still having that error? Could specify which OS, shell and trimAl version are you using? What @scapella suggested should work fine (trimal -in t1.fas -out t2.fas -selectcols { 0-592,4268-5581 }).

Thank you for your feedback!
Nicolás