by word list
word_list_grep.pl
#if $searchwhere.choice == "column":
-c $searchwhere.column
#end if
-o $output
$inverse
$caseinsensitive
$wholewords
$skip_first_line
$wordlist
$input
**What it does**
This tool selects lines that match words from a word list.
--------
**Example**
Input file (UCSC's rmsk track from dm3)::
585 787 66 241 11 chrXHet 2860 3009 -201103 - DNAREP1_DM LINE Penelope 0 594 435 1
585 1383 78 220 0 chrXHet 3012 3320 -200792 - DNAREP1_DM LINE Penelope -217 377 2 1
585 244 103 0 0 chrXHet 3737 3776 -200336 - DNAREP1_DM LINE Penelope -555 39 1 1
585 2270 83 144 0 chrXHet 7907 8426 -195686 + DNAREP1_DM LINE Penelope 1 594 0 1
585 617 189 73 68 chrXHet 10466 10671 -193441 + DNAREP1_DM LINE Penelope 368 573 -21 1
586 1122 71 185 0 chrXHet 173138 173322 -30790 - PROTOP DNA P -4033 447 230 1
...
...
Word list file::
STALKER
PROTOP
Output sequence (searching in column 11)::
586 1122 71 185 0 chrXHet 173138 173322 -30790 - PROTOP DNA P -4033 447 230 1
586 228 162 0 0 chrXHet 181026 181063 -23049 + STALKER4_I LTR Gypsy 9 45 -6485 1
585 245 105 26 0 chr3R 41609 41647 -27863406 + PROTOP_B DNA P 507 545 -608 4
586 238 91 0 0 chr3R 140224 140257 -27764796 - PROTOP_B DNA P -617 536 504 4
...
...
( With **find whole-words** not selected, *PROTOP* matched *PROTOP_B*, *STALKER* matched *STALKER4_I* )
Output sequence (searching in column 11, and whole-words only)::
586 670 90 38 57 chrXHet 168356 168462 -35650 - PROTOP DNA P -459 4021 3918 1
586 413 139 70 0 chrXHet 168462 168548 -35564 - PROTOP DNA P -3406 1074 983 1
586 1122 71 185 0 chrXHet 173138 173322 -30790 - PROTOP DNA P -4033 447 230 1
...
...