output from ABI

Charles Bailey bailey at genetics.upenn.edu
Tue Jun 7 14:32:56 EST 1994

In article <7JUN199409353262 at seqvax.caltech.edu>, mathog at seqvax.caltech.edu (David Mathog) writes:
> In article <2t1u9i$59d at hippo.shef.ac.uk>, mb1gt at silver.shef.ac.uk (G Turner) writes...
>>Does anyone have experience of using gcg in conjunction with 
>>the ABI automated sequencing machine.  Is there anyway the 
>>MACintosh files generated by the machine can be viewed by 
>>gcg or associated software?
>>If not, does anyone have experience of using staden for the 
>>same purpose?
> There is nothing in 7.3 that will let you read the trace file.  If you have
> generated .seq files then you can run REFORMAT on them to get them into GCG
> format.  As I recall, these are just straight sequence, so you'll get the 
> "no .." warning message, but the REFORMAT will complete.

You may also have to run ChopUp, depending on how you get files to the system
running GCG.  Here's a little DCL procedure we use to streamline this; it
should be easy to write a shell script to do this under Unix as well.

                    Charles Bailey

!              Computational Biology and Informatics Laboratory
!         Dept. of Genetics, Univ. of Pennsylvania School of Medicine
!              Philadelphia, PA USA 19104     Tel. (215) 573-3112
!          Internet: bailey at genetics.upenn.edu  (IN
$! Brief DCL routine to convert raw output files from ABI 733 sequencer into
$! format compatible with GCG
$! P1 = ABI data file
$! P2 = GCG sequence file
$ get_raw: If P1 .eqs. "" Then -
      Read/Prompt="Name of file to be converted: " Sys$Command P1
$ If P1 .eqs. "" Then Goto get_raw
$ get_gcg: If P2 .eqs. "" Then -
       Read/Prompt="Name of GCG sequence file: " Sys$Command P2
$ If P2 .eqs. "" Then Goto get_gcg
$ Write Sys$Output ""
$ Write Sys$Output "Converting file using GCG utilities..."
$ Write Sys$Output ""
$ seqname = F$Parse(P1,,,"NAME")
$ outfl1 = seqname + ".DAT"
$ outfl2 = seqname + ".TSQ_TMP$$"
$! Set up GCG environment if necessary
$ If F$TrnLNM("GenCoreDisk") .eqs. "" Then GCG
$ Chopup/Infile='P1'/Outfile='outfl1'/NoMonitor/NoDoc
$ Reformat/Infile='outfl1'/Outfile='P2'/NoMonitor/NoDoc
$ Delete/NoLog 'outfl1';
$ Exit

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