In article <17MAY199317433948 at bioch.tamu.edu>, whitsitt at bioch.tamu.edu (Mark S. Whitsitt, N5RJF) writes:
> I am wondering if anyone has written or knows of a VMS command file or
> executable which will automate the submission of stringsearches etc. as batch
> jobs. The GCG package we use does not have the '/batch' option for
> stringsearch and the users of the computers in our lab are not necessarily able
> or interested in learning how to create command files for batch submission. I
> can write this myself, but figured, why reinvent the wheel?
>> Thanks
>> Mark S. Whitsitt, N5RJF Texas A&M University, Dept of Biochemistry
> Internet: mwhitsitt at tamu.edu College Station, Tx. 77843-2128
> AMPRnet: n5rjf at n5rjf.ampr.org (409) 845-0832
> Packet/APLINK: N5RJF @ KE5HE.TX.USA.NA
Here's an update I did (two years ago, though) of Steve Clark's shell.
Since you're on the internet, you'd be better off doing such searches via
gopher.
Fote
=========================================================================
Foteos Macrides Worcester Foundation for Experimental Biology
MACRIDES at SCI.WFEB.EDU 222 Maple Avenue, Shrewsbury, MA 01545
=========================================================================
$!------------------------ CUT HERE -------------------------------------
$ orig_veri = f$environment("VERIFY_PROCEDURE")
$ v = f$verify(0) ! (StringSearch turns off verification)
$
$ ! STRINGSEARCH.COM
$
$ ! June 7, 1991 -- Foteos Macrides MACRIDES at WFEB2.BITNET
$ MACRIDES at SCI.WFEB.EDU
$
$ ! This procedure helps the user execute the GCG program STRINGSEARCH.
$ ! The program is run interactively, and the actual search is done in
$ ! batch mode.
$
$ ! Based on STRINGS.COM for GCG V6:
$ ! Written by Steve Clark
$ ! Samuel Lunenfeld Research Institute
$ ! Mt. Sinai Hospital, Toronto, Canada
$ ! Modifications by F.M. for GCG V7:
$ ! Properly handles strings with quotes, e.g., " globin" to get hits
$ ! for words beginning with globin (and exclude hemoglobin).
$ ! Accepts list files.
$ ! Gets /MATCH qualifier if relevant.
$ ! Submits both "definitions" and "complete sequence record" searches
$ ! to batch.
$
$ ! Installation:
$ !
$ ! Define command in GENETICS.COM:
$! $ If f$mode() .eqs. "INTERACTIVE" then -
$! String*Search :== @device:[directory]StringSearch
$ !
$ ! Create queue in SYSTARTUP_V5.COM:
$! $ INITIALIZE/QUEUE/START/BATCH/JOB_LIMIT=1/BASE_PRIORITY=3 STRIN$BATCH
$ !
$ ! Define queue-query command in SYLOGIN.COM:
$! $ STQ :== "SHOW QUEUE/ALL STRIN$BATCH "
$
$ on control_y then goto terminate
$ bell[0,7] = 7
$ ws := "write sys$output"
$ iq := inquire/nopunctuation
$
$ ws ""
$ ws "STRINGSEARCH finds sequences by searching sequence library"
$ ws "documentation for character patterns such as 'globin' or 'Human'."
$ ws ""
$ ws "STRINGSEARCH can search either definitions or complete sequence"
$ ws "records. The records take 100 times as long to search as the"
$ ws "catalogue. If you specify more than one word to search for,"
$ ws "(separated by commas) you will have the option to seek entries"
$ ws "that contain all the specified words, any one of them, or a
$ ws "minimum number of them."
$ ws ""
$ ws "STRINGSEARCH through which database?"
$ ws ""
$ ws "1) GenEMBL (GE)"
$ ws "2) GenBank (GB)"
$ ws "3) EMBL (EM)"
$ ws "4) Swiss-Prot (SW)
$ ws "5) PIR-Protein (PIR)"
$ ws "6) PIR-Nucleic (NUCL)"
$ ws "7) VecBase (VEC)"
$ ws "8) Let me use my own list file (e.g., @MYFILE.LIST)
$ ws ""
$ database := ""
$ myfile := ""
$ mode := ""
$ outfile := ""
$
$get_database:
$
$ iq choice "Please choose one (* 1 *): "
$ if(choice.EQS."") then choice := 1
$ if(choice.EQS."1") then database := GE
$ if(choice.EQS."2") then database := GB
$ if(choice.EQS."3") then database := EM
$ if(choice.EQS."4") then database := SW
$ if(choice.EQS."5") then database := PIR
$ if(choice.EQS."6") then database := NUCL
$ if(choice.EQS."7") then database := VEC
$ if(choice.EQS."8") then goto get_list
$ if(database.EQS."GE") then goto get_genemblset
$ if(database.NES."") then goto ask_subset
$ ws "''bell'"
$ ws "Valid choices are 1,2,3,4,5,6,7 or 8."
$ goto get_database
$
$get_list:
$
$ iq choice "Please specify the list file (e.g., MYFILE.LIST): "
$ if(choice.EQS."") then goto get_list
$ if(f$locate("@",choice).NE.0) then myfile := 'choice'
$ if f$search(myfile) .eqs. "" then goto myfile_not_found
$ if(myfile.NES."") then database := "@''myfile'"
$ if(database.NES."") then goto get_searcharea
$ ws "''bell'"
$ ws "Re-enter the file name without an @."
$ goto get_list
$
$myfile_not_found:
$
$ ws "''bell'"
$ ws "''myfile' does not exist."
$ ws ""
$ goto get_list
$
$get_genemblset:
$
$ ! Find out which of the GenEMBL databases should be searched, or
$ ! if all of them should be.
$
$ ws ""
$ ws "GenEMBL sequence set to search:"
$ ws " 1) All of the sequences (GE)"
$ ws " 2) Primate sequences (PR)"
$ ws " 3) Rodent sequences (RO)"
$ ws " 4) Other Mammalian sequences (OM)"
$ ws " 5) Other Vertebrate sequences (OV)"
$ ws " 6) Invertebrate sequences (IN)"
$ ws " 7) Plant sequences (PL)"
$ ws " 8) Bacterial sequences (BA)"
$ ws " 9) Organelle sequences (OR)"
$ ws "10) Phage sequences (PH)"
$ ws "11) Viral sequences (VI)"
$ ws "12) Structural RNA sequences (ST)"
$ ws "13) Synthetic sequences (SY)"
$ ws "14) Unannotated sequences (UN)"
$ ws ""
$
$ask_genemblset:
$
$ iq choice "Please enter choice (* 1 *): "
$ if(choice.EQS."") then choice := 1
$ database := ""
$ if(choice.EQS."1") then database := GE
$ if(choice.EQS."2") then database := PR
$ if(choice.EQS."3") then database := RO
$ if(choice.EQS."4") then database := OM
$ if(choice.EQS."5") then database := OV
$ if(choice.EQS."6") then database := IN
$ if(choice.EQS."7") then database := PL
$ if(choice.EQS."8") then database := BA
$ if(choice.EQS."9") then database := OR
$ if(choice.EQS."10") then database := PH
$ if(choice.EQS."11") then database := VI
$ if(choice.EQS."12") then database := ST
$ if(choice.EQS."13") then database := SY
$ if(choice.EQS."14") then database := UN
$ if(database.NES."") then goto ask_subset
$ ws "''bell'"
$ ws "Valid responses are 1 - 14, inclusive."
$ goto ask_genemblset
$
$ask_subset:
$
$ ! Find out if a subset of the database should be searched
$
$ subset := "*"
$ ws ""
$ ws "How much of ''database' do you want to search?"
$ ws ""
$ ws "1) All of it (i.e., ''database':*)."
$ ws "2) Only a subset (e.g., ''database':HUM*)."
$ ws ""
$
$ask_subset_choice:
$
$ iq choice "Please enter your choice (* 1 *): "
$ if(choice.EQS."") then goto get_searcharea
$ if(choice.EQS."1") then goto get_searcharea
$ if(choice.EQS."2") then goto get_subset
$ choice := ""
$ ws "''bell'Valid choices are 1 or 2."
$ goto ask_subset_choice
$
$get_subset:
$
$ ! Find out what subset of the database to search
$
$ ws ""
$ iq subset "Specify the ''database' subset to search (e.g., HUM*): "
$ if(subset.NES."") then goto get_searcharea
$ ws "''bell'Invalid answer."
$ ws "If you want to search the whole database, type *"
$ goto get_subset
$
$get_searcharea:
$
$ ! See which part of the sequence headers to peruse.
$
$ ws ""
$ ws "Do you want to search through:"
$ ws ""
$ ws "1) Definitions"
$ ws "2) Complete sequence records"
$ ws ""
$
$ask_searcharea:
$
$ iq choice "Please choose one (* 1 *): "
$ if(choice.EQS."") then choice := 1
$ if(choice.EQS."1") then mode := "DEFINITIONS_ONLY"
$ if(choice.EQS."2") then mode := "COMPLETE_RECORDS"
$ if(mode.NES."") then goto get_text
$ ws "''bell'"
$ ws "Valid choices are 1 or 2."
$ goto ask_searcharea
$
$get_text:
$
$ !
