Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
comparison orthologs/ucsb_hamster/lib/wisecfg/wise.per @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
| author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
|---|---|
| date | Tue, 11 Mar 2014 12:19:13 -0700 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:5b9a38ec4a39 |
|---|---|
| 1 ! this is the wise config file | |
| 2 ! for you to fool around with Remember ! lines are comments | |
| 3 ! and keys should go flush with the left hand margin | |
| 4 ! | |
| 5 ! All wise.cfg's at the moment should have interactive key | |
| 6 ! | |
| 7 interactive | |
| 8 ! | |
| 9 ! This is the linkfile designation (for searchwise/swise) | |
| 10 ! | |
| 11 linkfile wise.links | |
| 12 ! | |
| 13 ! The next lines show a UNIX style background system | |
| 14 ! | |
| 15 queuecommand nice nohup csh | |
| 16 addamperstand | |
| 17 ! | |
| 18 ! | |
| 19 viewlength 20 | |
| 20 ! | |
| 21 ! view command for pairwise.... | |
| 22 viewer more | |
| 23 ! | |
| 24 !viewbackground | |
| 25 ! | |
| 26 ! | |
| 27 !The next two keys give default codon and matrix files | |
| 28 !I'm using here the fact that pairwise/searchwise will open files | |
| 29 !from WISECONFIGDIR if it can't open the file as the straight filename | |
| 30 ! | |
| 31 codondefault codon.table | |
| 32 matrixdefault blosum62.bla | |
| 33 ! | |
| 34 ! | |
| 35 ! The next lines give default for all situations gap and ext | |
| 36 ! and other parameters | |
| 37 ! | |
| 38 gapdefault 1900 | |
| 39 extdefault 200 | |
| 40 framedefault 2500 | |
| 41 frameextdefault 2000 | |
| 42 stopdefault 500 | |
| 43 ! | |
| 44 !The next lines gives default specific for profiles or protein sequences | |
| 45 !I've found these values by rule of thumb. These values will superceed | |
| 46 ! the defaults above | |
| 47 ! | |
| 48 gap_pro 2200 | |
| 49 ext_pro 200 | |
| 50 gap_seq 700 | |
| 51 ext_seq 70 | |
| 52 ! | |
| 53 !This gives the number of cells to report in PairWise | |
| 54 ! | |
| 55 reportrate 10000 | |
| 56 ! | |
| 57 !This tells the screen length in PairWise/Opensearch help files | |
| 58 ! | |
| 59 screenlength 20 | |
| 60 ! | |
| 61 !These give help files | |
| 62 ! | |
| 63 localhtmlhelp http://www.sanger.ac.uk/~birney/wise/help/ | |
| 64 ! | |
| 65 ! This gives the SRS link and library links | |
| 66 ! | |
| 67 srslink http://www.sanger.ac.uk/srs/srsc? | |
| 68 srslibrary +-l+swissprot+-l+embl+-l+swissnew+-l+emnew | |
| 69 ! | |
| 70 ! This gives the sort of extensions to append to output file | |
| 71 ! in searchwise | |
| 72 ! | |
| 73 outputappend .out | |
| 74 htmlappend .html | |
| 75 alignhtmlappend _aln.html | |
| 76 alignappend .aln | |
| 77 ! | |
| 78 pairmainhelp pairmain.hlp | |
| 79 pairalignhelp pairaln.hlp | |
| 80 confighelp pairconfig.hlp | |
| 81 ! | |
| 82 protopmenuhelp buildprofile.hlp | |
| 83 promatrixmenuhelp pwmatrix.hlp | |
| 84 proweightmenuhelp pwweights.hlp | |
| 85 progapmenuhelp pwgap.hlp | |
| 86 ! | |
| 87 searchmainhelp searchmain.hlp | |
| 88 searchparahelp searchaln.hlp | |
| 89 searchsubmithelp searchsubmit.hlp | |
| 90 ! | |
| 91 ! | |
| 92 ! | |
| 93 stagger 500 | |
| 94 highscore 250 | |
| 95 align 50 | |
| 96 ! | |
| 97 deletecom | |
| 98 ! | |
| 99 ! | |
| 100 ! | |
| 101 hard_linkage | |
| 102 | |
| 103 | |
| 104 |