Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate orthologs/ucsb_hamster/lib/wisecfg/wise.per @ 0:5b9a38ec4a39 draft default tip

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