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5000+ seqs in GCG...

mathog at seqaxp.bio.caltech.edu mathog at seqaxp.bio.caltech.edu
Tue Mar 7 16:04:51 EST 1995


In article <PMR.95Mar3133059 at unst.sanger.ac.uk>, pmr at unst.sanger.ac.uk (Peter Rice) writes:
>
>But having done that, how do you plan to edit the alignment you get?
>

I've got a partial solution - modifications to REFORMAT that let it
do certain column operations on .MSF{*}, .fil, or *.seq sequences. It
adds these 4 command line options.

/BEGin           beginning of range, defaults to 1
/END             end of range, defaults to Maximum sequence length
/DELete          delete the subsequence in the range, leave the rest
/REVerse         return the reverse strand

Ie,

$!     delete columns 1 through 10 from all entries
$ reformat/infile=all.msf{*}/outfile=short.msf/msf/begin=1/end=10/delete
$!
$!     select only columns 10 through 100 from all entries
$ reformat/infile=all.msf{*}/outfile=short.msf/msf/begin=10/end=100
$!
$!     ditto, but for a pile of sequence files
$ reformat/infile=*.seq/outfile=short.msf/msf/begin=10/end=100
$!

We had to come up with this when dealing with alignments of thousands of 
tRNAs.  It's only been tested on VMS at GCG V8.0, but it should work on
Unix too. 

If anybody wants the modifications send me e-mail or I could post them if
there's enough demand.

Regards,

David Mathog
mathog at seqvax.bio.caltech.edu
Manager, sequence analysis facility, biology division, Caltech 



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