How do I list all the tools included in FAST ?

[tseemann]

Besides typing {fas,gb,aln} and pressing is there any way I can find out all the tools available?

I think it needs something like wossname or tfm in the EMBOSS package.

Maybe the simplest thing would be

• a man page for "fast"
• running "fast"

Both of these would list each tool and short description (the man NAME line?), one per line:

% fast
FASTA
faswc - tally sequences and characters
fasuniq - Remove duplicate sequence records in a multifasta file or datastream.
fastail
...
GENBANK
gbfalncut
gbfcut
...
ALIGNMENT
alnpi
alncut
...

[dhard]

We have this already written ("man fast" lists all the executables) so we'll make sure it gets installed in the next release.

On Jun 5, 2015, at 8:08 PM, Torsten Seemann notifications@github.com wrote:

Besides typing {fas,gb,aln} and pressing is there any way I can find out all the tools available?

I think it needs something like wossname or tfm in the EMBOSS package.

Maybe the simplest thing would be

• a man page for "fast" • running "fast" Both of these would list each tool and short description (the man NAME line?), one per line: % fast FASTA faswc - tally sequences and characters fasuniq - Remove duplicate sequence records in a multifasta file or datastream. fastail ... GENBANK gbfalncut gbfcut ... ALIGNMENT alnpi alncut ...

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David H. Ardell Assistant Professor, Molecular Cell Biology Unit Chair, Quantitative and Systems Biology Program 5200 North Lake Road, School of Natural Sciences, University of California, Merced CA 95343 office: SE 228 // (209) 228-2953 // fax: (209) 228-4675 // http://compbio.ucmerced.edu/ardell OFFICE HOURS FOR BIO 2 and QSB: Tuesdays and Thursdays, 1:30 pm to 2:30 pm or by appt.

[tseemann]

A command as well would be good so you can "fast | grep dup" for example.

[dhard]

Yes. This is already written. I'm fixing this in a new release, I will try to release this coming week.

Dave

On Jun 13, 2015, at 4:35 PM, Torsten Seemann notifications@github.com wrote:

A command as well would be good so you can "fast | grep dup" for example.

— Reply to this email directly or view it on GitHub.

David H. Ardell Assistant Professor, Molecular Cell Biology Unit Chair, Quantitative and Systems Biology Program 5200 North Lake Road, School of Natural Sciences, University of California, Merced CA 95343 office: SE 228 // (209) 228-2953 // fax: (209) 228-4675 // http://compbio.ucmerced.edu/ardell OFFICE HOURS FOR BIO 2 and QSB: Tuesdays and Thursdays, 1:30 pm to 2:30 pm or by appt.

[tseemann]

Thanks Dave.