Question about READSEQ on a VAX

Lee F. Kolakowski lfk at eastman1.mit.edu
Sun Mar 1 14:49:14 EST 1992

On 1 Mar 92 03:02:00 GMT,
agoodrid at vaxa.weeg.uiowa.edu (Stephen Klautky) said:
> Dan Jacobson wrote in bionet.software (for unix):

>> readseq -a -f5 epd29.seq | cat > epd29.gcg

>> Filtering it through cat is important as otherwise it will output each
>> sequence into a seperate file.  This assumes that you are using unix.
This is not correct

readseq -h as
readSeq (14Nov91), multi-format molbio sequence reader.
usage: readseq [-ailcCvpf] in.seq [-oOut.seq] > out.seq
    -a     select All sequences
    -i#    select Item number from several
    -l     List sequences only
    -v     Verbose progress
    -c     change to lower case
    -C     change to UPPER CASE
    -oOut.seq  redirect Output
    -p     Pipe (command line, <stdin, >stdout)
    -f#    Format number for output,  or
    -fName Format name for output:
         1. IG/Stanford            8. Pearson/Fasta   
         2. GenBank/GB             9. Zuker           
         3. NBRF/PIR              10. Olsen           
         4. EMBL                  11. Phylip3.4/Phylip
         5. GCG                   12. Phylip3.3/Interleaved
         6. DNAStrider            13. Plain/Raw       
         7. Fitch                                     

So this suggests that
>> readseq -a -f5 epd29.seq | cat > epd29.gcg

should be for Unix
	readseq -f5 -a -p epd29.seq  > epd29.gcg

where as 
	readseq -f5 -a -p -oepd29.gcg   epd29.seq

as -ofilename causes all output to be written to filename

Frank Kolakowski

| Email: lfk at eastman1.mit.edu or kolakowski at helix.mgh.harvard.edu or  |
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| Lee F. Kolakowski                                                   |
| Endocrine Unit                    Massachusetts General Hospital    |
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