grep searching

Michael Myers myersm at rockvax.rockefeller.edu
Fri Feb 14 00:21:30 EST 1997


I have been experimenting with the different SRS servers, most recently
SRS 5 at Heidelberg. First, let me say it is wonderful service. The new
View Manager is amazing. Now if I could just get to the point where I
could save some results! Here are my questions (SRS 5 at EMBL unless
otherwise mentioned).

Is it allowable to connect grep expressions with boolean operators?

for a single indice (eg. AllText): /^expression1$/ | /^expression2 $/

Since the manual says that all entries get converted to regular
expressions anyway, I thought this would work. I never get data back, so
I'm not sure if I'm trying to do something illegal or if the software
isn't working properly.

Here is a simple example to show some of the other troubles I'm having. I
tried this expression and it returned a regex error (note that there is a
space prior to the hyphen in the character set):

In order to match "T cell" or "T-cell"

/^t[ -]cell$/

(I discovered that the above expression does work from the EBI SRS server)

The following just uses wildcards, but it fails to return any matches when
I know that it should.

t?lymphocyte | t?cell

If I just search for "lymphocyte", I get some records which contain
"T-lymphocyte" or "T-cell".

I can't figure out why so many of my search terms fail.

I also tried /^t.cell$/ from the EBI server and it worked fine.

However, when I tried to join two searches (described below) from the
Query Manager page, I got another error. 

Given the following searches:

Q6 (retrieval) := "[Sequence-AllText:/^t[- ]cell$/] |
[Sequence-AllText:/^t[- ]lymphocyte$/] |
[Sequence-AllText:thymocyte]" found 303 entries 
       303 entries from SWISSPROT 
Q7 (retrieval) := "[Sequence-Organism:human]" found 4000 entries 
       4000 entries from SWISSPROT 

q6 & q7 returns the error:

syntax error, at "cell$/] | [Sequence-AllText:/^t[- ]lymphocyte$/] |
[Sequence-AllText:thymocyte]" 


Thanks for any clarification,

Mike Myers

Michael Myers
Laboratory of Genetics
The Rockefeller University
212-327-8233  (-7420 fax)
myersm at rockvax.rockefeller.edu




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