FastDNAML for DEC ALPHA running VMS?

Brian Fristensky frist at ccu.umanitoba.ca
Fri Dec 9 16:35:52 EST 1994


In article 0712941302300001 at 131.158.31.163, MSALMINEN_at_WRAIR__GUDE__1 at mail.hjf.org (Mika Salminen) writes:
> While I'm at it, has anyone added fastDNAml to GDE on a Sun, and where could that
> version be found?

Here's my .GDEmenus item for fastDNAml, along with a csh script that creates an 
infile, using the parameters set in the menu. Like the PHYLIP programs, fastDNAml
can only work with files named infile, outfile and treefile. To make it possible
for more than one job to run at a time, each fastDNAml job runs in a
uniquely-named temporary directory. Output can go to treetool, DRAWTREE, or a textfile. 

#------------------------- fastDNAml ( 8/ 8/94)  --------------------------
# menu by Brian Fristensky, Univ. of Manitoba (frist at cc.umanitoba.ca)
item:fastDNAml
# sed edits out ":CDS" that is added to CDS sequence names extracted by FEATURES
#If your sequence names do not contain a string in the form ":*", it will
#have no effect.
itemmethod:mkdir in1.dir; sed "s/[:].*//" in1 | readseq -a -f12 -pipe | sed "s/ YF//1" > in1.dir/infile.tmp; rm in1; cd in1.dir; (fastDNAml.csh infile.tmp $QADD $BSTRAP $BSEED $GLOBAL $JMBLE $JSEED $TRATIO $SPOUT $OUTGRP > infile; rm infile.tmp; $PREEDIT fastDNAml <infile > outfile; sed "s/\[.*\] //" treefile.* | tr -d "'" >treefile; $WHERE) &
itemhelp:fastDNAml/fastDNAml_doc.txt

arg:GLOBAL
arglabel:DO GLOBAL REARRANGEMENTS?
argtype:chooser
argchoice:Yes:Y
argchoice:No:N
argvalue:0

arg:QADD
arglabel:QUICKADD?
argtype:chooser
argchoice:Yes:Y
argchoice:No:N
argvalue:0

arg:TRATIO
arglabel:TRANSITION/TRANSVERSION RATIO
argtype:text
argtext:2.0

arg:BSTRAP
arglabel:BOOTSTRAP THE DATA?
argtype:chooser
argchoice:Yes:Y
argchoice:No:N
argvalue:0

arg:BSEED
argtype:slider
arglabel:Bootstrap random number seed
argmin:0
argmax:65535
argvalue:12345

arg:JMBLE
arglabel:JUMBLE (RANDOMIZE) SEQUENCE ADDITION ORDER?
argtype:chooser
argchoice:Yes:Y
argchoice:No:N
argvalue:0

arg:JSEED
argtype:slider
arglabel:Jumble random number seed
argmin:0
argmax:65535
argvalue:12345

arg:SPOUT
arglabel:SPECIFY AN OUTGROUP?
argtype:chooser
argchoice:Yes:Y
argchoice:No:N
argvalue:1

arg:OUTGRP
arglabel:Sequence # of outgroup:
argtype:text
argtext:

arg:PREEDIT
arglabel:EDIT THE DATA BEFORE RUNNING fastDNAml?
argtype:chooser
argchoice:Yes:textedit infile;
argchoice:No:
argvalue:1

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Treetool:mv outfile ../in1.outfile; mv treefile ../in1.treefile; cd ..; rm -r in1.dir; (textedit in1.outfile; rm in1.outfile) & (treetool in1.treefile; rm in1.treefile) &
argchoice:Drawtree:mv outfile ../in1.outfile; (cd ..; textedit in1.outfile; rm in1.outfile)& (cp $dat/Phylip/font1 fontfile; drawtree.csh l r 0 360 360 yes 0.2 0.14286 |drawtree; $GDE_PSVIEW plotfile; cd ..; rm -r in1.dir) &
argchoice:Output files:mv outfile ../$OUTNAME.outfile; mv treefile ../$OUTNAME.treefile; cd ..; rm -r in1.dir
argvalue:0
 
arg:OUTNAME
arglabel:raw name
argtype:text

in:in1
informat:genbank
insave:

----------------------------- fastDNAml.csh ---------------------------------
#!/bin/csh

#Version  8/ 6/94
# Set up infile for fastDNAml
#Synopsis: fastDNAml.csh infile qadd bstrap bseed global jmble jseed 
#                        tratio spout outgrp| fastDNAml

#Convert arguments to variables
set INFILE      = $1
set QADD        = $2
set BSTRAP      = $3
set BSEED       = $4
set GLOBAL      = $5
set JMBLE       = $6
set JSEED       = $7
set TRATIO      = $8
set SPOUT       = $9
set OUTGRP      = $10

#----------------- generate first line for infile -----------------

set FIRSTLINE = `head -1 $INFILE`
set FIRSTLINE = "$FIRSTLINE Y F T"
if ($QADD == Y) set FIRSTLINE = "$FIRSTLINE Q"
if ($GLOBAL == Y) set FIRSTLINE = "$FIRSTLINE G"
if ($BSTRAP == Y) set FIRSTLINE = "$FIRSTLINE B"
if ($JMBLE == Y)  set FIRSTLINE = "$FIRSTLINE J"
if ($SPOUT == Y)  set FIRSTLINE = "$FIRSTLINE O"


#---------------- Write first line and optional command lines------
echo $FIRSTLINE
echo T $TRATIO
if ($BSTRAP == Y) echo B $BSEED
if ($JMBLE == Y) echo J $JSEED
if ($SPOUT == Y)  echo O $OUTGRP

#--------------- Write sequence part of file ----------------------
tail +2 $INFILE







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