.GDEmenus code for ClustalW

L. H. Bell lhb at s-ind1.dl.ac.uk
Wed Dec 7 08:23:19 EST 1994


In article <3c2qm8$dq4 at decaxp.harvard.edu>, robison at nucleus.harvard.edu (Keith Robison) writes:
|> Has anyone out there interfaced ClustalW to GDE?  Did you write specific
|> menus?  Could I steal them?
|>

Heres one - it writes the clustalw command line into a shell script so it can be run
in batch. It was written for the SGI version of gde output into.

Hope this helps,

Lachlan Bell
SEQNET

http://www.dl.ac.uk/SEQNET/home.html

(PS, if you spot any 'features' please e-mail them to me.)


#********** 
item: clustalw
#********** 
# 
# Run clustalw. Open output file with  editor. Run another gde with 
# clustalw output as input. Remove all created files! 
#
# Did funny naming of arguments because gde was getting confused with
# variables that with similar names or the same names as in previous items:
#
# Supposedly takes gde format but I get 'Sequence format is unknown' when I try
#
itemmethod:(readseq in1 -a -p -f=nbrf>in1.cl;header.sh>in1.com; echo  clustalw /output=GDE /outfile=$NAM /outorder=$ORDER /CASE=$BZA /infile=in1.cl /PWMATRIX=$XX /PWGAPOPEN=$YY /PWGAPEXT=$ZZ /align /MATRIX=$WW /GAPOPEN=$STZZ /GAPEXT=$TS /ENDGAPS=$CGH /GAPDIST=$KIK $PAS $HYDRO /MAXDIV=$EYQ /SCORE=$MNE /TYPE=$ASDA $TRANS \> in1.rpt>>in1.com; $BATCH)&

itemhelp:clustalw_help

in:in1
informat:genbank

arg:BATCH
argtype:choice_menu
arglabel:Submit to batch?
argchoice:Big:echo $RM in1* >> in1.com ;qsub -q big in1.com
argchoice:Small:echo $RM in1* >> in1.com ;qsub -q fast in1.com
argchoice:Interactive: echo '$REPORT' >> in1.com ; chmod 0700 in1.com ; in1.com ;$RM in1.cl in1.com ;$GDE $NAM
argvalue:0

arg:NAM
argtype:text
arglabel:Put output in which file?
argtext:clustalw_out

arg:ASDA
argtype:chooser
arglabel:Sequence type?
argchoice:Protein:PROTEIN
argchoice:DNA/RNA:DNA

arg:REPORT
argtype:chooser
arglabel:View assembly report?
argchoice:No:
argchoice:Yes:/exe1/bin/emacs in1.rpt&

arg:BZA
argtype:chooser
arglabel:Should the residues be in -
argchoice:Upper Case:upper
argchoice:Lower Case:lower

arg:ORDER
argtype:choice_menu
arglabel:Should the output order be -
argvalue:0
argchoice:Same as input order:input
argchoice:In alignment order:aligned

arg:XX
argtype:choice_menu
arglabel:Use what matrix for pairwise aligning
argvalue:2
argchoice:PAM:PAM
argchoice:MD:MD
argchoice:BLOSUM:BLOSUM

arg:WW
argtype:choice_menu
arglabel:Use what matrix for multiple aligning
argvalue:2
argchoice:PAM:PAM
argchoice:MD:MD
argchoice:BLOSUM:BLOSUM

arg:YY
argtype:slider
arglabel:gap open penalty (pairwise)
argmin:1
argmax:100
argvalue:10

arg:ZZ
argtype:text
arglabel:gap extending penalty (pairwise) [0.0-1.0]
argtext:0.10

arg:STZZ
argtype:slider
arglabel:gap open penalty (multiple)
argmin:1
argmax:100
argvalue:10

arg:TS
argtype:text
arglabel:gap extending penalty (multiple) [0.0-1.0]
argtext:0.5

arg:TRANS
argtype:chooser
arglabel:DNA transitions weighted?
argvalue:0
argchoice:No:
argchoice:Yes:/TRANSITIONS

arg:CGH
argtype:chooser
arglabel:Penalise end gaps?
argvalue:0
argchoice:No:NO
argchoice:Yes:YES

arg:HYDRO
argtype:chooser
arglabel:Hydrophilic gaps?
argvalue:0
argchoice:On:
argchoice:Off:/NOHGAP

arg:PAS
argtype:chooser
arglabel:Pascarella gaps?
argvalue:
argchoice:On:
argchoice:Off:/NOPGAP

arg:MNE
arg:argtype:choice_menu
arglabel:Scoring Method
argchoice:Absolute:absolute
argchoice:Percentage:percentage

arg:KIK
argtype:slider
arglabel:gap separation penalty range?
argmin:1
argmax:100
argvalue:8

arg:EYQ
argtype:slider
arglabel:% ident. for delay?
argmin:1
argmax:100
argvalue:40

#
# This takes a list as the argument therefore can't do
#
#arg:HRES
#argtype:chooser
#arglabel:List hydrophilic residues?
#argvalue:0
#argchoice:No:
#argchoice:Yes:/HGAPRESIDUES

-----------start of header.sh
#!/bin/csh -f
# this first line needed
echo "#\!/bin/csh -f"
# set up movement to the current directory. This will be the one with
# the input file in it.
echo cd $cwd
# the program & parameters are echoed from control line in gde
------------end of header.sh




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