home *** CD-ROM | disk | FTP | other *** search
/ Crawly Crypt Collection 1 / crawlyvol1.bin / apps / science / readseq / add.gde next >
Text File  |  1992-12-30  |  2KB  |  124 lines
  1. #
  2. # dgg added new readseq formats, 29 dec 92
  3. #
  4.  
  5. item:Export Foreign Format
  6. itemmethod:readseq in1 -pipe -all -form=$FORMAT > $OUTPUTFILE
  7. itemhelp:readseq.help
  8.  
  9. arg:FORMAT
  10. argtype:choice_menu
  11. argchoice:GenBank:genbank
  12. argchoice:IG/Stanford:ig
  13. argchoice:NBRF:nbrf
  14. argchoice:EMBL:embl
  15. argchoice:GCG:gcg
  16. argchoice:DNA Strider:strider
  17. argchoice:Fitch:fitch
  18. argchoice:Pearson/Fasta:pearson
  19. argchoice:Zuker:zuker
  20. argchoice:Olsen:olsen
  21. argchoice:Phylip:phylip
  22. #argchoice:Phylip v3.2:phylip3.2
  23. argchoice:Plain text:raw
  24. argchoice:ASN.1:asn
  25. argchoice:PIR:pir
  26. argchoice:MSF:msf
  27. argchoice:PAUP:paup
  28. argchoice:Pretty:pretty -nametop -nameleft=3 -numright -nameright -numtop
  29.  
  30. arg:OUTPUTFILE
  31. argtype:text
  32. arglabel:Save as?
  33.  
  34. in:in1
  35. informat:genbank
  36.  
  37.  
  38. #
  39. #dgg addition for new readseq, 24 dec 92
  40. #
  41.  
  42. item:Pretty Print
  43. itemmethod:readseq in1 -p -a -f=pretty $NAMELEFT $NAMERIGHT $NUMTOP $NUMBOT $NUMLEFT $NUMRIGHT -col=$COLS -width=$WIDTH $MATCH $GAPC > in1.pretty; (textedit in1.pretty; /bin/rm -f in1 in1.pretty)&
  44. itemhelp:readseq.help
  45.  
  46. #nametop is bad !?
  47.  
  48. in:in1
  49. informat:genbank
  50.  
  51. arg:NAMETOP
  52. argtype:chooser
  53. arglabel:Names at top  ?
  54. argchoice:No:
  55. argchoice:Yes:-nametop
  56.  
  57. arg:NAMELEFT
  58. argtype:chooser
  59. arglabel:Names at left ?
  60. argchoice:No:
  61. argchoice:Yes:-nameleft
  62.  
  63. arg:NAMERIGHT
  64. argtype:chooser
  65. arglabel:Names at right?
  66. argchoice:Yes:-nameright
  67. argchoice:No:
  68.  
  69. arg:NUMTOP
  70. argtype:chooser
  71. arglabel:Numbers at top  ?
  72. argchoice:Yes:-numtop
  73. argchoice:No:
  74.  
  75. arg:NUMBOT
  76. argtype:chooser
  77. arglabel:Numbers at tail ?
  78. argchoice:No:
  79. argchoice:Yes:-numbot
  80.  
  81. arg:NUMLEFT
  82. argtype:chooser
  83. arglabel:Numbers at left ?
  84. argchoice:Yes:-numleft
  85. argchoice:No:
  86.  
  87. arg:NUMRIGHT
  88. argtype:chooser
  89. arglabel:Numbers at right?
  90. argchoice:Yes:-numright
  91. argchoice:No:
  92.  
  93. arg:MATCH
  94. argtype:chooser
  95. arglabel:Use match '.' for 2..n species?
  96. argchoice:No:
  97. argchoice:Yes:-match
  98.  
  99. arg:GAPC
  100. argtype:chooser
  101. arglabel:Count gap symbols?
  102. argchoice:No:
  103. argchoice:Yes:-gap
  104.  
  105. arg:WIDTH
  106. argtype:slider
  107. arglabel:Sequence width?
  108. argmin:10
  109. argmax:200
  110. argvalue:50
  111.  
  112. arg:COLS
  113. argtype:slider
  114. arglabel:Column spacers?
  115. argmin:0
  116. argmax:50
  117. argvalue:10
  118.  
  119.  
  120. ### pretty print insert end
  121. #
  122.  
  123.  
  124.