RICE@EMBL.BITNET (Peter Rice) (02/07/90)
Michael W. Clarke asks: >I have had a request for the annotation that accompanies sequences in the >databases (specifically the citation to the published paper). Is there any >way in which this info can be retrieved without having to FETCH the entire >sequence into a file? Is there such a thing as a /NOSEQUENCE switch for >FETCH? Should there be? Many thanks for any and all help in advance. A direct hit on one of my favourite improvement requests. I use a modified FETCH all the time to check reference information or to read the feature table. It is really simple to implement. You need read access to the GCG source code, so call your system manager if the source code is not loaded, or is protected. If you don't understand the procedure below, ask your system manager to help you. $ GCG $ COPY GENSOURCE:FETCH.FOR SHOWDATA.FOR $ EDIT SHOWDATA.FOR .. comment out (or delete) the line that does a "Call WriteSeq" .. for example, add an exclamation or a "C" at the start of the line Call WriteSeq(OutFile, Strand, InFName) .. changes to ! Call WriteSeq(OutFile, Strand, InFName) $ FOR SHOWDATA $ SHARELINK SHOWDATA "sharelink" is a GCG utility that gives your program access to the GCG procedure libraries. Then add this to your login.com, or type it when you need it: $ SHOWDATA :== $ disk:[directory]SHOWDATA /OUT=GCGSTDOUT "disk" and "directory" are the disk and directory where you have been working. You must include them here, otherwise the VAX will look in the wrong place. This defines a SHOWDATA command just like the TYPEDATA command in GCG, but with your new version of the program that doesn't write the sequence. If you leave the "/OUT=GCGSTDOUT" out of the line above, you will be defining a new FETCH (writing the annotation information to a file instead of to the terminal). This fix only works for entries in databases. SHOWDATA will still print the sequence for individual sequence files - they take a little more effort to fix. Adding a "/NOSEQ" or even a "/NOREF" to the command is also fairly easy if you know just a little Fortran - or you can use the same approach as above to take out the line that writes the reference information (Call CopyHeading) and make another local version of FETCH (again, just as long as you are only interested in database entries and not in individual sequence files - FETCH just copies the whole file for them, for database entries it does the copy in three stages) Peter Rice ----------------------------------------------------------------------------- Peter Rice, EMBL | Post: BioComputing Programme | European Molecular EARN/Bitnet: rice@embl.bitnet | Biology Laboratory Internet: rice%embl.bitnet@cunyvm.cuny.edu | Postfach 10-2209 | D-6900 Heidelberg Phone: +49-6221-387247 | West Germany