Example use of SRS on mac. d.g.gilbert, 29apr95, gilbertd@bio.indiana.edu based on SRS version 4.02 Files included in mac distribution: SRSodd, SRSbuild, SRSgetz, SRSwgetz, in 68K and PPC processor versions -- all the applications. These need to reside in the main level folder for use, as they will look for :data:, :index:, :etc: and other needed files in those named subfolders. in :codewar-projects: +SRSodd, +SRSbuild, ... -- Codewarrior project files. Move to main folder to use. in :etc: message.dat -- required for all programs (error messages) :mac: -- srswin.sec and srswin.ptr are built here by SRSodd in :srs: -- full SRS source w/ modifications for Mac use in :odd: -- full SRS odd set, with mods for Mac and for dgg work in :data: :pir: pir1.dat, pir2.dat, pir3.dat :flygenes: genes.txt -- Example data files in :index: -- build indices here Archive files ------------ 8863 Apr 30 10:28 SRS-on-mac-help this file 425242 Apr 30 10:35 srs4-mac-68k-apps.hqx applications for 68K/any mac 510995 Apr 30 10:52 srs4-mac-ppc-apps.hqx applications for PowerPC mac 567282 Apr 30 10:45 srs4-mac-etc.hqx accessory files (etc,www,data,...) 70478 Apr 30 10:56 srs4-mac-odd.tar.gz odd files 52334 Apr 30 10:52 srs4-mac-odd.diff odd file differences from SRS v4.02 325585 Apr 30 10:54 srs4-mac-src.tar.gz source files 44757 Apr 30 10:52 srs4-mac-src.diff source file diff.s from SRS v4.02 Comments on building programs ------------------------------ Use CodeWarrior version 4 or later. Codewarrior 3.x won't work because it doesn't support MPW Newline syntax. I don't have advice for building w/ ThinkC or with MPW development systems on mac, except that it is important to use MPW Newline syntax (where \n and \r are swapped for file i/o), or else all the .sdl and data files will have to have newlines as the unix LF character instead of the mac CR character. Use the codewarrior4 project files to build. If you want to recreate one of these project files, preference settings include Language: MPW Newlines Project: allocate plenty of memory (5000 k or more if you index large data files) 68K Processor: 4byte ints, far data In file "srsos.h" the BOOTSTRAP needs to be uncommented by hand to build the SRSodd program, then outcommented to build the other programs. //srsos.h #elif MAC ... /* BOOTSTRAP is only for SRSodd program */ /*#define BOOTSTRAP 1 */ The file "srsenv-mac.c" creates what is needed to replace "getenv()" for finding parts of the SRS system at runtime. This is where the relative paths to folders are set. I've added an output formatting routine, genes4report.c, for use with flygene data. I think this is currently active for wgetz but not for getz. Steps to test binaries ---------------------- 1. Build :etc:mac:srswin.sec SRSodd> -sd srswin (this is the equivalent of "srssection" on unix) ........ ________________________________________________________________________________ made section files: "SRSSEC:srswin.sec" with 370 blocks 2. Build and compress data indices SRSbuild> pir SRSbuild> -c pir SRSbuild> flygene SRSbuild> -c flygene SRSbuild> -c pir ...wrote IDs file ":index:pir_id.ids" size: 1 kbytes, IDs: 48...wrote IDs file ":index:pir_acc.ids" size: 1 kbytes, IDs: 58...wrote IDs file ":index:pir_def.ids" size: 2 kbytes, IDs: 343...wrote IDs file ":index:pir_org.ids" size: 1 kbytes, IDs: 140...wrote IDs file ":index:pir_dat.ids" size: 1 kbytes, IDs: 49...wrote IDs file ":index:pir_key.ids" size: 1 kbytes, IDs: 135...wrote IDs file ":index:pir_ref.ids" size: 9 kbytes, IDs: 1995...wrote IDs file ":index:pir_cc.ids" size: 1 kbytes, IDs: 41...wrote IDs file ":index:pir_fts.ids" size: 1 kbytes, IDs: 31...wrote IDs file ":index:pir_sl.ids" size: 1 kbytes, IDs: 49 3. Check libraries SRSbuild> libs SRSbuild> -info pir Library: "PIR" from group: "Sequence" Data Fields (B=busy, C=compressed): Name Short Type Inx Ids No No Creation B C Name (kb) (kb) Words IDs Date ------------------------------------------------------------------------ ID ID id 1 0 48 0 4/29/95 0 0 AllText ALL group Accession ACC index 1 0 58 58 4/29/95 0 1 Definition DEF index 4 1 179 343 4/29/95 0 1 Organism ORG index 2 0 90 140 4/29/95 0 1 Date DAT num 1 0 30 49 4/29/95 0 1 Keywords KEY index 1 0 53 135 4/29/95 0 1 Reference REF index 20 8 906 1995 4/29/95 0 1 Comment CC index 1 0 36 41 4/29/95 0 1 Features FTS index 0 0 23 31 4/29/95 0 1 SeqLength SL num 1 0 45 49 4/29/95 0 1 Links: read-link "FLYGENE" to "PIR" Directory: "devc:srs:data:pir:" Filename(s): pir1.dat pir1.dat pir2.dat pir2.dat pir3.dat pir3.dat 4. Test getz & wgetz SRSgetz> [pir-all:cytochrome] 10 entries written to set "q1" PIR1: ! ID: 01000002 PIR1:CCCZ ! ID: 02000002 PIR1:CCMQR ! ID: 03000002 PIR1:QXBY34 ! ID: 04000002 PIR1:QQBY2M ! ID: 05000002 PIR1:QXASC ! ID: 08000002 PIR1:QXASD ! ID: 09000002 PIR1:QXASF ! ID: 0a000002 PIR2:S29350 ! ID: 15000002 PIR2:S11172 ! ID: 16000002 SRSgetz> [pir-id:QXBY34] -td ENTRY QXBY34 #type fragment TITLE DNA endonuclease I-SceII - yeast (Saccharomyces cerevisiae) mitochondrion (strain D273-10B) (SGC2) (fragment) ALTERNATE_NAMES DNA endonuclease aI4; gene oxi3 intron 4 protein; intron-encoded protein aI4 ORGANISM #formal_name mitochondrion Saccharomyces cerevisiae DATE 15-Nov-1984 #sequence_revision 30-Jun-1993 #text_change 27-Jun-1994 ACCESSIONS A04511 REFERENCE A92267 #authors Bonitz, S.G.; Coruzzi, G.; Thalenfeld, B.E.; Tzagoloff, A.; Macino, G. #journal J. Biol. Chem. (1980) 255:11927-11941 #title Assembly of the mitochondrial membrane system. Structure and nucleotide sequence of the gene coding for subunit 1 of yeast cytochrome oxidase. #cross-references MUID:81069885 #accession A04511 ##molecule_type DNA ##residues 1-475 ##label BON ##cross-references EMBL:V00694 ##note we have reassigned the boundaries of introns 1, 2 by homology with other cytochrome-c oxidase chain I sequences; the authors' translation differs from the sequence shown in lacking 57-Val, in having 69-Cys, and in having an additional Thr after 69-Cys ##note the authors translated the codon ATA for residue 87 according to the standard code GENETICS #map_position 43.7-55.1 #genome mitochondrion #genetic_code SGC2 #introns 57/1; 69/1; 81/3 CLASSIFICATION #superfamily mRNA maturase bI4 KEYWORDS endonuclease; mitochondrion FEATURE 1-240 #domain cytochrome-c oxidase chain I (exons 1 to 4) #label EXN\ 241-475 #domain intron-encoded domain #label INT SUMMARY #length 475 #checksum 1255 >QXBY34 YLLPLMIGAT DTAFPRINNI AFWVLPMGLV CLVTSTLVES GAGTGWTVYP PLSSIQAHSG PSVDLAIFAL HLTSISSLLG AINFIVTTLN MRTNGMTMHK LPLFVWSIFI TAFLLLLSLP VLSAGITMLL LDRNFNTSFF EVAGGGDPIL YEHLFWFFGQ TVATIIMLMM YNDMHFSKCW KLLKKWITNI MSTLFKALFV KMFMSYNNQQ DKMMNNTMLK KDNIKRSSET TRKMLNNSMN KKFNQWLAGL IDGDGYFGIV SKKYVSLEIT VALEDEMALK EIQNKFGGSI KLRSGVKAIR YRLTNKTGMI KLINAVNGNI RNTKRLVQFN KVCILLGIDF IYPIKLTKDN SWFVGFFDAD GTINYSFKNN HPQLTKTVTN KYLQDVQEYK NILGGNIYFD KSQNGYYKWS IQSKDMVLNF INDYIKMNPS RTTKMNKLYL SKEFYNLKEL KAYNKSSDSM QYKAWLNFEN KWKNK SRSwgetz> [flygene-all:AcrF]
Gene symbol                  : Acr96Ac
Last update                  : 24 Feb 95      
Synonym(s)                   : AcrF
                             : sbd
Full name                    : Acetylcholine receptor 96Ac
FlyBase gene id number       : FBgn0004118
Genetic map position         : 3-[83]
Cytological map position     :
    96A
Function(s) of product       : transmembrane protein
                             : acetylcholine-receptor-beta2-subunit
Prosite protein domains      : PS00236 == Neurotransmitter-gated ion-channels signature.
D. mel. DNA/RNA AC no(s)     : X55676 
D. mel. protein AC no(s)     : PIR/S12899 
                             : SWP/P25162 
Reference FBrf0051780 reports the following clone data:
   Cyto. location of clone   : 96A3
   cDNA clone length         : 1.8
   Transcript size(s)        : 2.0
   RNA space/time distrib.   : Late embryos, late pupae.
   Open reading frame size   : 493 aa
Phenotypic information       :
    Acr96Ac is expressed at high levels during late embryonic and
    late
    pupal stages, the transcripts are localized in the CNS.