From: CZJ@CU.NIH.GOV
Newsgroups: bionet.molbio.genbank
Subject: shell for retrieve
Date: 30 Dec 92 13:52:21 GMT
Distribution: bionet

I have written a shell for Word Perfect with accompanying macro
for retrieving GenBank, etc. entries from the NCBI mail server.
The shell is a text editor that reminds the user to enter the
proper values.  The macro then extracts that information needed
by the mail server and puts that info in a separate document.
The file can then be saved and sent off to NCBI for processing.

The document is fairly self-explanatory.  The attributes
(i.e. [LOC], [KEY], etc.) look best when transferred to four
columns (one for each database) using word perfect's column
feature.  In my shell I have also highlighted those items
that do not get sent to ncbi.  I have also underlined the default
values.

The macro to pull the relevant information out of the shell is
as follows:
---------------------------------------------------
{home} {home} up arrow    :goes to top of document
{control} {home} |        :goes to first vertical bar
{right arrow}             :
{Alt F4}
{control home} |          :goes to second vertical bar
{left arrow}
{control F4}
1
2
{shift F3}
{Enter}

The file can then be saved as a text file using control F5, etc.
------------------

Jim Cassatt

The shell I use is as follows:
---------------------------------------------------
DATABASES

genbank  gbupdate  embl     emblupdate  swissprot  pir
vector   genpept   gpupdate kabatnuc    kabatpro   tfd
|
DATALIB
MAXDOCS 20
MAXLINES 1000
TITLES no/yes
STARTDOC 1
BEGIN

|
GenBank

[DEF]
[LOC]
[ACC]
[SEG]
[SRC]
[REF]
[COM]
[FEA]
[ORG]EMBL

[DEF]
[LOC]
[ACC]
[KEY]
[DAT]
[SRC]
[DXR]
[REF]
[COM]
[FEA]
[BAS]SWISS-PROT

[DEF]
[LOC]
[ACC]
[KEY]
[DAT]
[GEN]
[SRC]
[CLS]
[ORG]
[REF]
[COM]
[FEA]
[DCR]
PIR

[DEF]
[ALT]
[SUM]
[DAT]
[SUP]
[ACC]
[HST]
[KEY]
[PLA]
[SRC]
[GEN]
[INC]
[REF]
[COM]
[FEA]

       #  GENBANK and GBUPDATE Field Descriptions
       #

       DEFINITION [DEF]
       LOCUS [LOC]
       ACCESSION NO. [ACC]
       KEYWORDS [KEY]
       SEGMENT [SEG]
       SOURCE [SRC]
       REFERENCE [REF]
       COMMENT[COM]
       FEATURES [FEA]
       BASE COUNT [BAS]
       ORIGIN [ORG]


       #  EMBL and EMBLUPDATE Field Descriptions
       #

       DEFINITION [DEF]
       ID [LOC]
       ACCESSION [ACC]
       KEYWORDS [KEY]
       DATES [DAT]
       SOURCE [SRC]
       CROSS-REF [DXR]
       REFERENCE [REF]
       COMMENT [COM]
       FEATURES [FEA]
       BASE COUNT [BAS]
       SEQUENCE


       #  SWISS-PROT Field Descriptions
       #

       DEFINITION [DEF]
       ID [LOC]
       ACCESSION [ACC]
       KEYWORDS [KEY]
       DATES [DAT]
       GENE NAME[GEN]
       SOURCE [SRC]
       ORGANISM CLASSIFICATION [CLS]
       ORGANELLE [ORG]
       REFERENCE [REF]
       COMMENT [COM]
       FEATURES [FEA]
       CROSS REFERENCE [DCR]
       SEQUENCE DATA
       SEQUENCE


       #  PIR Protein Data Base (NBRF)
       #

       DEFINITION [DEF]
       ALT-NAME [ALT]
       SUMMARY [SUM]
       DATE [DAT]
       SUPERFAMILY [SUP]
       ACCESSION NO [ACC]
       HOST [HST]
       KEYWORDS [KEY]
       PLACEMENT [PLA]
       SOURCE [SRC]
       GENETICS [GEN]
       INCLUDES [INC]
       REFERENCE [REF]
       COMMENT [COM]
       FEATURES [FEA]
       SEQUENCE


 
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