/var/lib/mobyle/programs/showseq.xml is in mobyle-programs 5.1.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 | <?xml version="1.0" encoding="ISO-8859-1"?>
<!-- XML Authors: Corinne Maufrais and Nicolas Joly, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>showseq</name>
<package>
<name>EMBOSS</name>
<version>6.3.1</version>
<doc>
<title>EMBOSS</title>
<description>
<text lang="en">European Molecular Biology Open Software Suite</text>
</description>
<authors>Rice,P. Longden,I. and Bleasby, A.</authors>
<reference>EMBOSS: The European Molecular Biology Open Software Suite (2000) Rice,P. Longden,I. and Bleasby, A. Trends in Genetics 16, (6) pp276--277</reference>
<sourcelink>http://emboss.sourceforge.net/download</sourcelink>
<homepagelink>http://emboss.sourceforge.net</homepagelink>
</doc>
</package>
<doc>
<title>showseq</title>
<description>
<text lang="en">Displays sequences with features in pretty format</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/showseq.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>display:nucleic:restriction</category>
<category>display:nucleic:translation</category>
<command>showseq</command>
</head>
<parameters>
<paragraph>
<name>e_input</name>
<prompt lang="en">Input section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_sequence</name>
<prompt lang="en">sequence option</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>EMBL</dataFormat>
<dataFormat>FASTA</dataFormat>
<dataFormat>GCG</dataFormat>
<dataFormat>GENBANK</dataFormat>
<dataFormat>NBRF</dataFormat>
<dataFormat>CODATA</dataFormat>
<dataFormat>RAW</dataFormat>
<dataFormat>SWISSPROT</dataFormat>
<dataFormat>GFF</dataFormat>
<card>1,n</card>
</type>
<format>
<code proglang="python">("", " -sequence=" + str(value))[value is not None]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>e_mfile</name>
<prompt lang="en">Restriction enzyme methylation data file (optional)</prompt>
<type>
<datatype>
<class>RestrictionEnzymeMethylationData</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="python">("", " -mfile=" + str(value))[value is not None ]</code>
</format>
<argpos>2</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_required</name>
<prompt lang="en">Required section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_format</name>
<prompt lang="en">Things to display</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>2</value>
</vdef>
<vlist>
<velem>
<value>0</value>
<label>Enter your own list of things to display</label>
</velem>
<velem>
<value>1</value>
<label>Sequence only</label>
</velem>
<velem>
<value>2</value>
<label>Default sequence with features</label>
</velem>
<velem>
<value>3</value>
<label>Pretty sequence</label>
</velem>
<velem>
<value>4</value>
<label>One frame translation</label>
</velem>
<velem>
<value>5</value>
<label>Three frame translations</label>
</velem>
<velem>
<value>6</value>
<label>Six frame translations</label>
</velem>
<velem>
<value>7</value>
<label>Restriction enzyme map</label>
</velem>
<velem>
<value>8</value>
<label>Baroque</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -format=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>e_things</name>
<prompt lang="en">Specify your own things to display (value from 1 to 100)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="python">e_format=="0"</code>
</precond>
<vdef>
<value>B,N,T,S,A,F</value>
</vdef>
<format>
<code proglang="python">("", " -things=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>4</argpos>
<comment>
<text lang="en">Specify a list of one or more code characters in the order in which you wish things to be displayed one above the other down the page.</text>
<text lang="en">S: Sequence</text>
<text lang="en">B: Blank line</text>
<text lang="en">1: Frame1 translation</text>
<text lang="en">2: Frame2 translation</text>
<text lang="en">3: Frame3 translation</text>
<text lang="en">-1: Compframe1 translation</text>
<text lang="en">-2: Compframe2 translation</text>
<text lang="en">-3: Compframe3 translation</text>
<text lang="en">T: Ticks line</text>
<text lang="en">N: Number ticks line</text>
<text lang="en">C: Complement sequence</text>
<text lang="en">F: Features</text>
<text lang="en">R: Restriction enzyme cut sites in forward sense</text>
<text lang="en">-R: Restriction enzyme cut sites in reverse sense</text>
<text lang="en">A: Annotation</text>
<text lang="en">For example if you wish to see things displayed in the order: sequence, complement sequence, ticks line, frame 1 translation, blank line; then you should enter 'S,C,T,1,B'.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_additional</name>
<prompt lang="en">Additional section</prompt>
<parameters>
<parameter>
<name>e_translate</name>
<prompt lang="en">Regions to translate (eg: 4-57,78-94)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -translate=" + str(value))[value is not None]</code>
</format>
<argpos>5</argpos>
<comment>
<text lang="en">Regions to translate (if translating).
If this is left blank the complete sequence is translated.
A set of regions is specified by a set of pairs of positions.
The positions are integers.
They are separated by any non-digit, non-alpha character.
Examples of region specifications are:
24-45, 56-78
1:45, 67=99;765..888</text>
</comment>
</parameter>
<parameter>
<name>e_revtranslate</name>
<prompt lang="en">Regions to translate in reverse direction (eg: 78-94,4-57)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -revtranslate=" + str(value))[value is not None]</code>
</format>
<argpos>6</argpos>
<comment>
<text lang="en">Regions to translate (if translating).
If this is left blank the complete sequence is translated.
A set of regions is specified by a set of pairs of positions.
The positions are integers.
They are separated by any non-digit, non-alpha character.
Examples of region specifications are:
78-56, 45-24,
888..765, 99=67; 45:1</text>
</comment>
</parameter>
<parameter>
<name>e_uppercase</name>
<prompt lang="en">Regions to put in uppercase (eg: 4-57,78-94)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -uppercase=" + str(value))[value is not None]</code>
</format>
<argpos>7</argpos>
<comment>
<text lang="en">Regions to put in uppercase.
If this is left blank, then the sequence case is left alone.
A set of regions is specified by a set of pairs of positions.
The positions are integers.
They are separated by any non-digit, non-alpha character.
Examples of region specifications are:
24-45, 56-78
1:45, 67=99;765..888
1,5,8,10,23,45,57,99</text>
</comment>
</parameter>
<parameter>
<name>e_highlight</name>
<prompt lang="en">Regions to colour in html (eg: 4-57 red 78-94 green)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -highlight=" + str(value))[value is not None]</code>
</format>
<argpos>8</argpos>
<comment>
<text lang="en">Regions to colour if formatting for HTML.
If this is left blank, then the sequence is left alone.
A set of regions is specified by a set of pairs of positions.
The positions are integers.
They are followed by any valid HTML font colour.
Examples of region specifications are:
24-45 blue 56-78 orange
1-100 green 120-156 red
A file of ranges to colour (one range per line) can be specified as '@filename'.</text>
</comment>
</parameter>
<parameter>
<name>e_annotation</name>
<prompt lang="en">Regions to mark (eg: 4-57 promoter region 78-94 first exon)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -annotation=" + str(value))[value is not None]</code>
</format>
<argpos>9</argpos>
<comment>
<text lang="en">Regions to annotate by marking.
If this is left blank, then no annotation is added.
A set of regions is specified by a set of pairs of positions followed by optional text.
The positions are integers.
They are followed by any text (but not digits when on the command-line).
Examples of region specifications are:
24-45 new domain 56-78 match to Mouse
1-100 First part 120-156 oligo
A file of ranges to annotate (one range per line) can be specified as '@filename'.</text>
</comment>
</parameter>
<parameter>
<name>e_enzymes</name>
<prompt lang="en">Comma separated restriction enzyme list</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>all</value>
</vdef>
<format>
<code proglang="python">("", " -enzymes=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>10</argpos>
<comment>
<text lang="en">The name 'all' reads in all enzyme names from the REBASE database. You can specify enzymes by giving their names with commas between then, such as: 'HincII,hinfI,ppiI,hindiii'.
The case of the names is not important. You can specify a file of enzyme names to read in by giving the name of the file holding the enzyme names with a '@' character in front of it, for example, '@enz.list'.
Blank lines and lines starting with a hash character or '!' are ignored and all other lines are concatenated together with a comma character ',' and then treated as the list of enzymes to search for.
An example of a file of enzyme names is:
! my enzymes
HincII, ppiII
! other enzymes
hindiii
HinfI
PpiI</text>
</comment>
</parameter>
<parameter>
<name>e_table</name>
<prompt lang="en">Genetic codes</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<vlist>
<velem>
<value>0</value>
<label>Standard</label>
</velem>
<velem>
<value>1</value>
<label>Standard (with alternative initiation codons)</label>
</velem>
<velem>
<value>2</value>
<label>Vertebrate mitochondrial</label>
</velem>
<velem>
<value>3</value>
<label>Yeast mitochondrial</label>
</velem>
<velem>
<value>4</value>
<label>Mold, protozoan, coelenterate mitochondrial and mycoplasma/spiroplasma</label>
</velem>
<velem>
<value>5</value>
<label>Invertebrate mitochondrial</label>
</velem>
<velem>
<value>6</value>
<label>Ciliate macronuclear and dasycladacean</label>
</velem>
<velem>
<value>9</value>
<label>Echinoderm mitochondrial</label>
</velem>
<velem>
<value>10</value>
<label>Euplotid nuclear</label>
</velem>
<velem>
<value>11</value>
<label>Bacterial</label>
</velem>
<velem>
<value>12</value>
<label>Alternative yeast nuclear</label>
</velem>
<velem>
<value>13</value>
<label>Ascidian mitochondrial</label>
</velem>
<velem>
<value>14</value>
<label>Flatworm mitochondrial</label>
</velem>
<velem>
<value>15</value>
<label>Blepharisma macronuclear</label>
</velem>
<velem>
<value>16</value>
<label>Chlorophycean mitochondrial</label>
</velem>
<velem>
<value>21</value>
<label>Trematode mitochondrial</label>
</velem>
<velem>
<value>22</value>
<label>Scenedesmus obliquus</label>
</velem>
<velem>
<value>23</value>
<label>Thraustochytrium mitochondrial</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -table=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>11</argpos>
</parameter>
<paragraph>
<name>e_featuresection</name>
<prompt lang="en">Feature display options</prompt>
<parameters>
<parameter>
<name>e_sourcematch</name>
<prompt lang="en">Source of feature to display</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -sourcematch=" + str(value))[value is not None]</code>
</format>
<argpos>12</argpos>
<comment>
<text lang="en">By default any feature source in the feature table is shown. You can set this to match any feature source you wish to show.
The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from.
The source may be wildcarded by using '*'.
If you wish to show more than one source, separate their names with the character '|', eg:
gene* | embl</text>
</comment>
</parameter>
<parameter>
<name>e_typematch</name>
<prompt lang="en">Type of feature to display</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -typematch=" + str(value))[value is not None]</code>
</format>
<argpos>13</argpos>
<comment>
<text lang="en">By default any feature type in the feature table is shown. You can set this to match any feature type you wish to show.
See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature types.
The type may be wildcarded by using '*'.
If you wish to show more than one type, separate their names with the character '|', eg:
*UTR | intron</text>
</comment>
</parameter>
<parameter>
<name>e_sensematch</name>
<prompt lang="en">Sense of feature to display (value from -1 to 1)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -sensematch=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to -1 is required</text>
</message>
<code proglang="python">value >= -1</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Value less than or equal to 1 is required</text>
</message>
<code proglang="python">value <= 1</code>
</ctrl>
<argpos>14</argpos>
<comment>
<text lang="en">By default any feature type in the feature table is shown. You can set this to match any feature sense you wish to show. 0 - any sense, 1 - forward sense, -1 - reverse sense</text>
</comment>
</parameter>
<parameter>
<name>e_minscore</name>
<prompt lang="en">Minimum score of feature to display</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.0</value>
</vdef>
<format>
<code proglang="python">("", " -minscore=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>15</argpos>
<comment>
<text lang="en">Minimum score of feature to display (see also maxscore)</text>
</comment>
</parameter>
<parameter>
<name>e_maxscore</name>
<prompt lang="en">Maximum score of feature to display</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.0</value>
</vdef>
<format>
<code proglang="python">("", " -maxscore=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>16</argpos>
<comment>
<text lang="en">Maximum score of feature to display.
If both minscore and maxscore are zero (the default), then any score is ignored</text>
</comment>
</parameter>
<parameter>
<name>e_tagmatch</name>
<prompt lang="en">Tag of feature to display</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -tagmatch=" + str(value))[value is not None]</code>
</format>
<argpos>17</argpos>
<comment>
<text lang="en">Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Some of these tags also have values, for example '/gene' can have the value of the gene name.
By default any feature tag in the feature table is shown. You can set this to match any feature tag you wish to show.
The tag may be wildcarded by using '*'.
If you wish to show more than one tag, separate their names with the character '|', eg:
gene | label</text>
</comment>
</parameter>
<parameter>
<name>e_valuematch</name>
<prompt lang="en">Value of feature tags to display</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -valuematch=" + str(value))[value is not None]</code>
</format>
<argpos>18</argpos>
<comment>
<text lang="en">Tag values are the values associated with a feature tag. Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Only some of these tags can have values, for example '/gene' can have the value of the gene name. By default any feature tag value in the feature table is shown. You can set this to match any feature tag value you wish to show.
The tag value may be wildcarded by using '*'.
If you wish to show more than one tag value, separate their names with the character '|', eg:
pax* | 10</text>
</comment>
</parameter>
<parameter>
<name>e_stricttags</name>
<prompt lang="en">Only display the matching tags</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -stricttags")[ bool(value) ]</code>
</format>
<argpos>19</argpos>
<comment>
<text lang="en">By default if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed. If this is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed.</text>
</comment>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>e_advanced</name>
<prompt lang="en">Advanced section</prompt>
<parameters>
<paragraph>
<name>e_remapsection</name>
<prompt lang="en">Restriction map options</prompt>
<parameters>
<parameter>
<name>e_flatreformat</name>
<prompt lang="en">Display re sites in flat format</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -flatreformat")[ bool(value) ]</code>
</format>
<argpos>20</argpos>
<comment>
<text lang="en">This changes the output format to one where the recognition site is indicated by a row of '===' characters and the cut site is pointed to by a '>' character in the forward sense, or a '<' in the reverse sense strand.</text>
</comment>
</parameter>
<parameter>
<name>e_mincuts</name>
<prompt lang="en">Minimum cuts per re (value from 1 to 1000)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">("", " -mincuts=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 1 is required</text>
</message>
<code proglang="python">value >= 1</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Value less than or equal to 1000 is required</text>
</message>
<code proglang="python">value <= 1000</code>
</ctrl>
<argpos>21</argpos>
<comment>
<text lang="en">This sets the minimum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut fewer times than this will be ignored.</text>
</comment>
</parameter>
<parameter>
<name>e_maxcuts</name>
<prompt lang="en">Maximum cuts per re</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>2000000000</value>
</vdef>
<format>
<code proglang="python">("", " -maxcuts=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>22</argpos>
<comment>
<text lang="en">This sets the maximum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut more times than this will be ignored.</text>
</comment>
</parameter>
<parameter>
<name>e_sitelen</name>
<prompt lang="en">Minimum recognition site length (value from 2 to 20)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>4</value>
</vdef>
<format>
<code proglang="python">("", " -sitelen=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 2 is required</text>
</message>
<code proglang="python">value >= 2</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Value less than or equal to 20 is required</text>
</message>
<code proglang="python">value <= 20</code>
</ctrl>
<argpos>23</argpos>
<comment>
<text lang="en">This sets the minimum length of the restriction enzyme recognition site. Any enzymes with sites shorter than this will be ignored.</text>
</comment>
</parameter>
<parameter>
<name>e_single</name>
<prompt lang="en">Force single re site only cuts</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -single")[ bool(value) ]</code>
</format>
<argpos>24</argpos>
<comment>
<text lang="en">If this is set then this forces the values of the mincuts and maxcuts qualifiers to both be 1. Any other value you may have set them to will be ignored.</text>
</comment>
</parameter>
<parameter>
<name>e_blunt</name>
<prompt lang="en">Allow blunt end re cutters</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noblunt", "")[ bool(value) ]</code>
</format>
<argpos>25</argpos>
<comment>
<text lang="en">This allows those enzymes which cut at the same position on the forward and reverse strands to be considered.</text>
</comment>
</parameter>
<parameter>
<name>e_sticky</name>
<prompt lang="en">Allow sticky end re cutters</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nosticky", "")[ bool(value) ]</code>
</format>
<argpos>26</argpos>
<comment>
<text lang="en">This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered.</text>
</comment>
</parameter>
<parameter>
<name>e_ambiguity</name>
<prompt lang="en">Allow ambiguous re matches</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noambiguity", "")[ bool(value) ]</code>
</format>
<argpos>27</argpos>
<comment>
<text lang="en">This allows those enzymes which have one or more 'N' ambiguity codes in their pattern to be considered</text>
</comment>
</parameter>
<parameter>
<name>e_plasmid</name>
<prompt lang="en">Allow circular dna</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -plasmid")[ bool(value) ]</code>
</format>
<argpos>28</argpos>
<comment>
<text lang="en">If this is set then this allows searches for restriction enzyme recognition site and cut positions that span the end of the sequence to be considered.</text>
</comment>
</parameter>
<parameter>
<name>e_methylation</name>
<prompt lang="en">Use methylation data</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -methylation")[ bool(value) ]</code>
</format>
<argpos>29</argpos>
<comment>
<text lang="en">If this is set then RE recognition sites will not match methylated bases.</text>
</comment>
</parameter>
<parameter>
<name>e_commercial</name>
<prompt lang="en">Only use restriction enzymes with suppliers</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nocommercial", "")[ bool(value) ]</code>
</format>
<argpos>30</argpos>
<comment>
<text lang="en">If this is set, then only those enzymes with a commercial supplier will be searched for. This qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through 'all' the enzymes in the REBASE database. It is assumed that, if you are asking for an explicit enzyme, then you probably know where to get it from and so all enzymes names that you have asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier.</text>
</comment>
</parameter>
<parameter>
<name>e_limit</name>
<prompt lang="en">Limits re hits to one isoschizomer</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nolimit", "")[ bool(value) ]</code>
</format>
<argpos>31</argpos>
<comment>
<text lang="en">This limits the reporting of enzymes to just one enzyme from each group of isoschizomers. The enzyme chosen to represent an isoschizomer group is the prototype indicated in the data file 'embossre.equ', which is created by the program 'rebaseextract'. If you prefer different prototypes to be used, make a copy of embossre.equ in your home directory and edit it. If this value is set to be false then all of the input enzymes will be reported. You might like to set this to false if you are supplying an explicit set of enzymes rather than searching 'all' of them.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<parameter>
<name>e_orfminsize</name>
<prompt lang="en">Minimum size of orfs (value greater than or equal to 0)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -orfminsize=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 0 is required</text>
</message>
<code proglang="python">value >= 0</code>
</ctrl>
<argpos>32</argpos>
<comment>
<text lang="en">This sets the minimum size of Open Reading Frames (ORFs) to display in the translations. All other translation regions are masked by changing the amino acids to '-' characters.</text>
</comment>
</parameter>
<parameter>
<name>e_threeletter</name>
<prompt lang="en">Display protein sequences in three-letter code</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -threeletter")[ bool(value) ]</code>
</format>
<argpos>33</argpos>
</parameter>
<parameter>
<name>e_number</name>
<prompt lang="en">Number the sequences</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -number")[ bool(value) ]</code>
</format>
<argpos>34</argpos>
</parameter>
<parameter>
<name>e_width</name>
<prompt lang="en">Width of sequence to display (value greater than or equal to 1)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>60</value>
</vdef>
<format>
<code proglang="python">("", " -width=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 1 is required</text>
</message>
<code proglang="python">value >= 1</code>
</ctrl>
<argpos>35</argpos>
</parameter>
<parameter>
<name>e_length</name>
<prompt lang="en">Line length of page (0 for indefinite) (value greater than or equal to 0)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -length=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 0 is required</text>
</message>
<code proglang="python">value >= 0</code>
</ctrl>
<argpos>36</argpos>
</parameter>
<parameter>
<name>e_margin</name>
<prompt lang="en">Margin around sequence for numbering (value greater than or equal to 0)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10</value>
</vdef>
<format>
<code proglang="python">("", " -margin=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 0 is required</text>
</message>
<code proglang="python">value >= 0</code>
</ctrl>
<argpos>37</argpos>
</parameter>
<parameter>
<name>e_name</name>
<prompt lang="en">Show sequence id</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noname", "")[ bool(value) ]</code>
</format>
<argpos>38</argpos>
<comment>
<text lang="en">Set this to be false if you do not wish to display the ID name of the sequence</text>
</comment>
</parameter>
<parameter>
<name>e_description</name>
<prompt lang="en">Show description</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nodescription", "")[ bool(value) ]</code>
</format>
<argpos>39</argpos>
<comment>
<text lang="en">Set this to be false if you do not wish to display the description of the sequence</text>
</comment>
</parameter>
<parameter>
<name>e_offset</name>
<prompt lang="en">Offset to start numbering the sequence from</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">("", " -offset=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>40</argpos>
</parameter>
<parameter>
<name>e_html</name>
<prompt lang="en">Use html formatting</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -html")[ bool(value) ]</code>
</format>
<argpos>41</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_output</name>
<prompt lang="en">Output section</prompt>
<parameters>
<parameter>
<name>e_outfile</name>
<prompt lang="en">Name of the output file (e_outfile)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>showseq.e_outfile</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>42</argpos>
</parameter>
<parameter isout="1">
<name>e_outfile_out</name>
<prompt lang="en">outfile_out option</prompt>
<type>
<datatype>
<class>ShowseqReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="python">e_outfile</code>
</filenames>
</parameter>
</parameters>
</paragraph>
<parameter ishidden="1">
<name>auto</name>
<prompt lang="en">Turn off any prompting</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">" -auto -stdout"</code>
</format>
<argpos>43</argpos>
</parameter>
</parameters>
</program>
|