In article <48dnd5$pi5 at lll-winken.llnl.gov>, Chris Barry
<chbarry at mackiller.llnl.gov> wrote:
> Is it possible to analyze ABI sequence files on GCG? or EGCG?
If the problem is flat-file format, you can run the file first through
chopup and the through reformat, or install the below command file to do
it in one step (remember to include a line such as $ chopgcg ==
"@[whatever-dir]chopgcg" in your login.com file in order for the command
to be recognized):
$!
$! CHOPGCG - a new command procedure to reformat flat-file
$! sequences in one step by passing them first through
$! the GCG program CHOPUP, and then through REFORMAT.
$!
$! Revision history: version 1.0 October 26, 1995
$!
$! Thanks for helpful suggestions to:
$!
$! Lynn Miller (Genetics Computer Group)
$! Dawn Cushing (Massachusetts General Hospital)
$! Several readers of the comp.os.vms and bionet.software.gcg newsgroups.
$!
$!
$!
$! Michael J. Coyne Jr.
$! Channing Laboratory
$! mjcoyne at warren.med.harvard.edu
$!
$!
$!
$ say :== write sys$output
$ say ""
$ say " CHOPGCG: This program reformats flat ASCII text"
$ say " files into GCG format in a single step."
$ say ""
$ say " Version 1.0 10/26/95 Michael J. Coyne"
$ say ""
$ say ""
$!
$!
$ on Control_y then goto end
$ on error then goto end
$!
$!
$ If P1 .eqs. ""
$ then
$ say ""
$ Inquire P1 "File to be formatted? "
$ say ""
$ If P1 .eqs. "" Then exit
$ EndIf
$!
$!
$ OrgFileName = P1
$!
$!
$ begin:
$!
$ IsThere = f$search(OrgFileName)
$ CurrentDir = f$directory()
$!
$ If (IsThere .eqs. "")
$ Then
$ say "Sorry, no file called ''OrgFileName' was found"
$ say "in the directory ''CurrentDir'."
$ say ""
$ Inquire OrgFileName "File to be formatted? "
$ say ""
$!
$ If (OrgFileName .eqs. "")
$ Then
$ exit
$ Else
$ goto begin
$ EndIf
$!
$ Else
$!
$ FileNameLength = (f$locate(".",OrgFileName))
$ FileExtLength = (f$length(OrgFileName) - (FileNameLength+1))
$ ShortFileName = f$extract(0,FileNameLength,OrgFileName)
$!
$ If (FileExtLength .eq. 0)
$ then FileExt = "SEQ"
$ else FileExt = f$extract((FileNameLength+1),FileExtLength,OrgFileName)
$ EndIf
$!
$ ChopFileName = "''ShortFileName'"+".CHOP"
$ FinalFileName = "''ShortFileName'"+".SEQ"
$!
$ Chopup /in='OrgFileName' /out='ChopFileName' /def
$ Reformat /in='ChopFileName' /out='FinalFileName' /def
$ Delete/nolog 'ChopFileName';*
$!
$ say ""
$ say "The file ''OrgFileName' has been reformatted for use with GCG."
$ say ""
$ say "The GCG formatted version has been saved as ''FinalFileName'"
$ say "in the directory ''CurrentDir'"
$ say ""
$!
$ EndIf
$ exit
