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/scripts/batch_ltrfinder.pl

http://dawg-paws.googlecode.com/
Perl | 1305 lines | 899 code | 195 blank | 211 comment | 42 complexity | 7c4e445dc5288d163469c5e9f3c9b652 MD5 | raw file
    

  1. #!/usr/bin/perl -w

    2. 

  2. #-----------------------------------------------------------+

    3. 

  3. #                                                           |

    4. 

  4. # batch_ltrfinder.pl - Run ltr_finder in batch mode         |

    5. 

  5. #                                                           |

    6. 

  6. #-----------------------------------------------------------+

    7. 

  7. #                                                           |

    8. 

  8. #  AUTHOR: James C. Estill                                  |

    9. 

  9. # CONTACT: JamesEstill_@_gmail.com                          |

    10. 

  10. # STARTED: 10/03/2007                                       |

    11. 

  11. # UPDATED: 10/03/2007                                       |

    12. 

  12. #                                                           |

    13. 

  13. # DESCRIPTION:                                              |

    14. 

  14. #  Run the ltr_finder program in batch mode.                |

    15. 

  15. #                                                           |

    16. 

  16. # VERSION: $Rev$                                            |

    17. 

  17. #                                                           |

    18. 

  18. # LICENSE:                                                  |

    19. 

  19. #  GNU General Public License, Version 3                    |

    20. 

  20. #  http://www.gnu.org/licenses/gpl.html                     |  

    21. 

  21. #                                                           |

    22. 

  22. #-----------------------------------------------------------+

    23. 

  23. # TO DO: -Reset vals to null and only print output when expected vals

    24. 

  24. #         are not null

    25. 

  25. #        -No gff output if no hits in ltr_finder

    26. 

  26. #        -Add possiblity to extract sequence data

    27. 

  27. 

    28. 

  28. package DAWGPAWS;

    29. 

  29. 

    30. 

  30. #-----------------------------+

    31. 

  31. # INCLUDES                    |

    32. 

  32. #-----------------------------+

    33. 

  33. use strict;

    34. 

  34. use Getopt::Long;

    35. 

  35. 

    36. 

  36. #-----------------------------+

    37. 

  37. # PROGRAM VARIABLES           |

    38. 

  38. #-----------------------------+

    39. 

  39. my ($VERSION) = q$Rev$ =~ /(\d+)/;

    40. 

  40. 

    41. 

  41. #-----------------------------+

    42. 

  42. # VARIABLE SCOPE              |

    43. 

  43. #-----------------------------+

    44. 

  44. my $indir;                     # Input dir of fasta files

    45. 

  45. my $outdir;                    # Base output dir 

    46. 

  46. my $config_file;               # Configuration file

    47. 

  47. 

    48. 

  48. # LTR Finder Parameters

    49. 

  49. my @lf_params = ();            # 2d Array to hold the find_ltr parameters 

    50. 

  50. 

    51. 

  51. # Booleans

    52. 

  52. my $quiet = 0;

    53. 

  53. my $verbose = 0;

    54. 

  54. my $show_help = 0;

    55. 

  55. my $show_usage = 0;

    56. 

  56. my $show_man = 0;

    57. 

  57. my $show_version = 0;

    58. 

  58. my $do_gff_convert = 0;

    59. 

  59. 

    60. 

  60. # Counters/Index Vals

    61. 

  61. my $i = 0;                     # Array index val

    62. 

  62. my $file_num = 0;              # File number

    63. 

  63. my $proc_num = 0;              # Process number

    64. 

  64. 

    65. 

  65. # Vars needing 

    66. 

  66. my $name_root;

    67. 

  67. my $gff_dir;

    68. 

  68. my $ls_out;

    69. 

  69. my $fl_gff_outpath;

    70. 

  70. 

    71. 

  71.  # Some options that would be useful to make ENV options

    72. 

  72. my $trna_db = $ENV{TRNA_DB};

    73. 

  73. my $prosite_dir = $ENV{PROSITE_DIR};

    74. 

  74. my $lf_path = $ENV{LTR_FINDER};

    75. 

  75. 

    76. 

  76. #-----------------------------+

    77. 

  77. # COMMAND LINE OPTIONS        |

    78. 

  78. #-----------------------------+

    79. 

  79. my $ok = GetOptions(# REQUIRED OPTIONS

    80. 

  80. 		    "i|indir=s"    => \$indir,

    81. 

  81.                     "o|outdir=s"   => \$outdir,

    82. 

  82. 		    "c|config=s"   => \$config_file,

    83. 

  83. 		    # ADDITIONAL OPTIONS

    84. 

  84. 		    "ltr-finder=s" => \$lf_path,     # LTR Finder Path

    85. 

  85. 		    "s|trna-db=s"  => \$trna_db,     # s as per program

    86. 

  86. 		    "a|prosite=s"  => \$prosite_dir, # a as per program

    87. 

  87. 		    "g|gff"        => \$do_gff_convert,

    88. 

  88. 		    "q|quiet"      => \$quiet,

    89. 

  89. 		    "verbose"      => \$verbose,

    90. 

  90. 		    # ADDITIONAL INFORMATION

    91. 

  91. 		    "usage"        => \$show_usage,

    92. 

  92. 		    "version"      => \$show_version,

    93. 

  93. 		    "man"          => \$show_man,

    94. 

  94. 		    "h|help"       => \$show_help,);

    95. 

  95. 

    96. 

  96. #-----------------------------+

    97. 

  97. # SHOW REQUESTED HELP         |

    98. 

  98. #-----------------------------+

    99. 

  99. if ($show_usage) {

    100. 

  100.     print_help("");

    101. 

  101. }

    102. 

  102. 

    103. 

  103. if ($show_help || (!$ok) ) {

    104. 

  104.     print_help("full");

    105. 

  105. }

    106. 

  106. 

    107. 

  107. if ($show_version) {

    108. 

  108.     print "\n$0:\nVersion: $VERSION\n\n";

    109. 

  109.     exit;

    110. 

  110. }

    111. 

  111. 

    112. 

  112. if ($show_man) {

    113. 

  113.     # User perldoc to generate the man documentation.

    114. 

  114.     system("perldoc $0");

    115. 

  115.     exit($ok ? 0 : 2);

    116. 

  116. }

    117. 

  117. 

    118. 

  118. # Throw error if required options not paseed

    119. 

  119. # Throw error if required arguments not present

    120. 

  120. if ( (!$indir) || (!$outdir) || (!$config_file) ) {

    121. 

  121.     print "\a";

    122. 

  122.     print STDERR "ERROR: An input directory must be specified" if !$indir;

    123. 

  123.     print STDERR "ERROR: An output directory must be specified" if !$outdir;

    124. 

  124.     print STDERR "ERROR: A config file must be specified" if !$config_file;

    125. 

  125.     print_help("full");

    126. 

  126.     exit;

    127. 

  127. }

    128. 

  128. 

    129. 

  129. #-----------------------------------------------------------+

    130. 

  130. # MAIN PROGRAM BODY                                         | 

    131. 

  131. #-----------------------------------------------------------+

    132. 

  132. 

    133. 

  133. #-----------------------------+

    134. 

  134. # CHECK FOR SLASH IN DIR      |

    135. 

  135. # VARIABLES                   |

    136. 

  136. #-----------------------------+

    137. 

  137. # If the indir does not end in a slash then append one

    138. 

  138. # TO DO: Allow for backslash

    139. 

  139. unless ($indir =~ /\/$/ ) {

    140. 

  140.     $indir = $indir."/";

    141. 

  141. }

    142. 

  142. 

    143. 

  143. unless ($outdir =~ /\/$/ ) {

    144. 

  144.     $outdir = $outdir."/";

    145. 

  145. }

    146. 

  146. 

    147. 

  147. #-----------------------------+

    148. 

  148. # CREATE THE OUT DIR          |

    149. 

  149. # IF IT DOES NOT EXIST        |

    150. 

  150. #-----------------------------+

    151. 

  151. unless (-e $outdir) {

    152. 

  152.     print "Creating output dir ...\n" if $verbose;

    153. 

  153.     mkdir $outdir ||

    154. 

  154. 	die "Could not create the output directory:\n$outdir";

    155. 

  155. }

    156. 

  156. 

    157. 

  157. #-----------------------------+

    158. 

  158. # LOAD THE CONFIG FILE        |

    159. 

  159. #-----------------------------+

    160. 

  160. $i=0;

    161. 

  161. my $config_line_num=0;

    162. 

  162. 

    163. 

  163. open (CONFIG, "<$config_file") ||

    164. 

  164.     die "ERROR Can not open the config file:\n $config_file";

    165. 

  165. 

    166. 

  166. while (<CONFIG>) {

    167. 

  167.     chomp;

    168. 

  168.     $config_line_num++;

    169. 

  169.     unless (m/^\#/) {

    170. 

  170.        	my @in_line = split (/\t/);           # Implicit split of $_ by tab

    171. 

  171. 	my $num_in_line = @in_line; 

    172. 

  172. 	

    173. 

  173. 	# Can have just a name for default

    174. 

  174. 	# or can have two columns with additional parameter options

    175. 

  175. 	if ($num_in_line < 3) { 

    176. 

  176. 	    $lf_params[$i][0] = $in_line[0] || "NULL";  # Name

    177. 

  177. 	    $lf_params[$i][1] = $in_line[1] || "";      # Suffix

    178. 

  178. #	    $lf_params[$i][2] = $in_line[2] || "NULL";  # MIN-MEM-DIST

    179. 

  179. #	    $lf_params[$i][3] = $in_line[3] || "NULL";  # MAX-MEM-DIST

    180. 

  180. #	    $lf_params[$i][4] = $in_line[4] || "NULL";  # MAX-MEM-GAP

    181. 

  181. #	    $lf_params[$i][5] = $in_line[5] || "NULL";  # MIN-LEN-LTR 

    182. 

  182. #	    $lf_params[$i][6] = $in_line[6] || "NULL";  # MAX-LEN-LTR

    183. 

  183. #	    $lf_params[$i][7] = $in_line[7] || "NULL";  # RANGE-BIN 

    184. 

  184. #	    $lf_params[$i][8] = $in_line[8] || "NULL";  # MIN LEN ORF

    185. 

  185. #	    $lf_params[$i][9] = $in_line[9] || "NULL";  # MAX E Value HMM

    186. 

  186. 	    $i++;

    187. 

  187. 	} # End of if $num_in_line is 10

    188. 

  188. 	else {

    189. 

  189. 	    print "\a";

    190. 

  190. 	    print STDERR "WARNING: Unexpected number of line in config".

    191. 

  191. 		" file line $config_line_num\n$config_file\n";

    192. 

  192. 	}

    193. 

  193. 

    194. 

  194.    } # End of unless comment line

    195. 

  195. } # End of while CONFIG file

    196. 

  196. close CONFIG;

    197. 

  197. 

    198. 

  198. # Number of parameter sets specified in the config file

    199. 

  199. my $num_par_sets = $i;

    200. 

  200. 

    201. 

  201. if ($num_par_sets == 0) {

    202. 

  202.     print "\a";

    203. 

  203.     print "ERROR: No parameter sets were found in the config file:\n".

    204. 

  204. 	"$config_file\n";

    205. 

  205.     exit;

    206. 

  206. }

    207. 

  207. 

    208. 

  208. #-----------------------------+

    209. 

  209. # Get the FASTA files from the|

    210. 

  210. # directory provided by the   |

    211. 

  211. # var $indir                  |

    212. 

  212. #-----------------------------+

    213. 

  213. opendir( DIR, $indir ) || 

    214. 

  214.     die "Can't open directory:\n$indir"; 

    215. 

  215. my @fasta_files = grep /\.fasta$|\.fa$/, readdir DIR ;

    216. 

  216. closedir( DIR );

    217. 

  217. my $num_files = @fasta_files;

    218. 

  218. 

    219. 

  219. if ($num_files == 0) {

    220. 

  220.     print "\a";

    221. 

  221.     print "ERROR: No input fasta files were found in the directroy:\n$indir\n";

    222. 

  222.     print "Fasta files must end with the fasta or fa extension\n";

    223. 

  223.     exit;

    224. 

  224. }

    225. 

  225. 

    226. 

  226. my $num_proc_total = $num_files * $num_par_sets;

    227. 

  227. 

    228. 

  228. print STDERR "$num_proc_total find_ltr runs to process\n" if $verbose;

    229. 

  229. 

    230. 

  230. 

    231. 

  231. 

    232. 

  232. 

    233. 

  233. 

    234. 

  234. 

    235. 

  235. for my $ind_file (@fasta_files) {

    236. 

  236. 

    237. 

  237.     $file_num++;

    238. 

  238. 

    239. 

  239.     # Get root file name

    240. 

  240.     if ($ind_file =~ m/(.*)\.fasta$/ ) {	    

    241. 

  241. 	$name_root = "$1";

    242. 

  242.     }  

    243. 

  243.     elsif ($ind_file =~ m/(.*)\.fa$/ ) {	    

    244. 

  244. 	$name_root = "$1";

    245. 

  245.     } 

    246. 

  246.     else {

    247. 

  247. 	$name_root = "UNDEFINED";

    248. 

  248.     }

    249. 

  249. 

    250. 

  250.     # The following added for temp work with gff output

    251. 

  251.     # 09/28/2007

    252. 

  252. #    if ($file_num == 5) {exit;}

    253. 

  253. #    print "Processing: $name_root\n";

    254. 

  254. 

    255. 

  255.     #-----------------------------+

    256. 

  256.     # CREATE ROOT NAME DIR        |

    257. 

  257.     #-----------------------------+

    258. 

  258.     my $name_root_dir = $outdir.$name_root."/";

    259. 

  259.     unless (-e $name_root_dir) {

    260. 

  260. 	mkdir $name_root_dir ||

    261. 

  261. 	    die "Could not create dir:\n$name_root_dir\n"

    262. 

  262.     }

    263. 

  263. 

    264. 

  264.     #-----------------------------+

    265. 

  265.     # CREATE LTR_FINDER OUTDIR    |

    266. 

  266.     #-----------------------------+

    267. 

  267.     # Dir to hold gene prediction output from local software

    268. 

  268.     my $ltrfinder_dir = $name_root_dir."ltr_finder/";

    269. 

  269.     unless (-e $ltrfinder_dir) {

    270. 

  270. 	mkdir $ltrfinder_dir ||

    271. 

  271. 	    die "Could not create ltr_finder out dir:\n$ltrfinder_dir\n";

    272. 

  272.     }

    273. 

  273. 

    274. 

  274.     #-----------------------------+

    275. 

  275.     # CREATE GFF OUTDIR           |

    276. 

  276.     #-----------------------------+

    277. 

  277.     if ($do_gff_convert) {

    278. 

  278. 	$gff_dir = $name_root_dir."gff/";

    279. 

  279. 	unless (-e $gff_dir) {

    280. 

  280. 	    mkdir $gff_dir ||

    281. 

  281. 		die "Could not create genscan out dir:\n$gff_dir\n";

    282. 

  282. 	}

    283. 

  283.     }

    284. 

  284. 

    285. 

  285. 

    286. 

  286.     #-----------------------------------------------------------+

    287. 

  287.     # RUN LTR_FINDER FOR EACH SET OF PARAM VALS IN CONFIG FILE |

    288. 

  288.     #-----------------------------------------------------------+

    289. 

  289.     for ($i=0; $i<$num_par_sets; $i++) {

    290. 

  290. 	

    291. 

  291. 	$proc_num++;

    292. 

  292. 	

    293. 

  293. 	# Load parameters from array refs to name vars

    294. 

  294. 	my $lf_gff_suffix = $lf_params[$i][0]; # Name of the parameter set

    295. 

  295. 	my $lf_cmd_suffix = $lf_params[$i][1]; # Name of the parameter set

    296. 

  296. 

    297. 

  297. 	print STDERR "#\n#------------------------------------\n" if $verbose;

    298. 

  298. 	print STDERR "#Processing: $name_root $lf_gff_suffix\n" if $verbose;

    299. 

  299. 	print STDERR "#------------------------------------\n" if $verbose;

    300. 

  300. 

    301. 

  301. 	# lf_out is path of the ltrfinder output file

    302. 

  302. 	my $lf_inseqpath = $indir.$ind_file;

    303. 

  303. 	my $lf_out = $ltrfinder_dir.$name_root."_".$lf_gff_suffix.

    304. 

  304. 	    "_ltr_finder.txt";

    305. 

  305. 	my $lf_gff_outpath = $gff_dir.$name_root."_".$lf_gff_suffix.

    306. 

  306. 	    "_ltr_finder.gff";

    307. 

  307. 	my $lf_cmd = "$lf_path $lf_inseqpath".

    308. 

  308. 	    " -s $trna_db".

    309. 

  309. 	    " -a $prosite_dir". 

    310. 

  310. 	    " $lf_cmd_suffix".

    311. 

  311. 	    " > $lf_out";

    312. 

  312. 

    313. 

  313. 	print STDERR "#\tCMD:$lf_cmd\n" if $verbose;

    314. 

  314. 

    315. 

  315. 	system ($lf_cmd);

    316. 

  316. 

    317. 

  317. 	#-----------------------------+

    318. 

  318. 	# CONVERT OUTPUT TO GFF       |

    319. 

  319. 	#-----------------------------+

    320. 

  320. 	if ( (-e $lf_out) && ($do_gff_convert)) {

    321. 

  321. 	    ltrfinder2gff ( $name_root, $lf_out, $lf_gff_outpath, 

    322. 

  322. 			    0, $lf_gff_suffix);

    323. 

  323. 	}

    324. 

  324. 

    325. 

  325.     }

    326. 

  326. 

    327. 

  327. 

    328. 

  328. 

    329. 

  329. } # End of for each individual fasta file

    330. 

  330. 

    331. 

  331. 

    332. 

  332. 

    333. 

  333. exit;

    334. 

  334. 

    335. 

  335. #-----------------------------------------------------------+ 

    336. 

  336. # SUBFUNCTIONS                                              |

    337. 

  337. #-----------------------------------------------------------+

    338. 

  338. 

    339. 

  339. sub print_help {

    340. 

  340. 

    341. 

  341.     # Print requested help or exit.

    342. 

  342.     # Options are to just print the full 

    343. 

  343.     my ($opt) = @_;

    344. 

  344. 

    345. 

  345.     my $usage = "USAGE:\n". 

    346. 

  346. 	"MyProg.pl -i InFile -o OutFile";

    347. 

  347.     my $args = "REQUIRED ARGUMENTS:\n".

    348. 

  348. 	"  --infile       # Path to the input file\n".

    349. 

  349. 	"  --outfile      # Path to the output file\n".

    350. 

  350. 	"\n".

    351. 

  351. 	"OPTIONS::\n".

    352. 

  352. 	"  --version      # Show the program version\n".     

    353. 

  353. 	"  --usage        # Show program usage\n".

    354. 

  354. 	"  --help         # Show this help message\n".

    355. 

  355. 	"  --man          # Open full program manual\n".

    356. 

  356. 	"  --quiet        # Run program with minimal output\n";

    357. 

  357. 	

    358. 

  358.     if ($opt =~ "full") {

    359. 

  359. 	print "\n$usage\n\n";

    360. 

  360. 	print "$args\n\n";

    361. 

  361.     }

    362. 

  362.     else {

    363. 

  363. 	print "\n$usage\n\n";

    364. 

  364.     }

    365. 

  365.     

    366. 

  366.     exit;

    367. 

  367. }

    368. 

  368. 

    369. 

  369. 

    370. 

  370. sub ltrfinder2gff {

    371. 

  371.     

    372. 

  372.     # seq_id could be extracted from the ltrfinder result

    373. 

  373.     # but passing it to the subfunction directly allows for cases

    374. 

  374.     # where the id assigned by ltr_struc differs from the way

    375. 

  375.     # the user is referring to the assembly

    376. 

  376.     # MAY WANT TO ALLOW FOR USING THE $ls_seq_id

    377. 

  377.     my ($seq_id, $lf_infile, $gffout, $do_append, $gff_suffix) = @_;

    378. 

  378.     

    379. 

  379.     # The gff src id

    380. 

  380.     my $gff_src = "ltr_finder:".$gff_suffix;

    381. 

  381.     my $gff_str_out;        # A single out string line of gff out

    382. 

  382. 

    383. 

  383.     # LTF FINDER COUTNERS/INDICES

    384. 

  384.     my $lf_id_num = 0;       # Incremented for every predicted model

    385. 

  385. 

    386. 

  386.     # LTR_FINDER BOOLEANS

    387. 

  387.     my $in_emp_details = 0;  # Exact match pairs details

    388. 

  388.     my $in_ltr_align = 0;    # Details of the LTR alignment

    389. 

  389.     my $in_pbs_align = 0;

    390. 

  390.     my $in_ppt;

    391. 

  391. 

    392. 

  392.     

    393. 

  393.     #

    394. 

  394.     my $lf_prog_name;             # LTR Finder program name

    395. 

  395.     my $lf_seq_id;                # Seq id

    396. 

  396.     my $lf_seq_len;               # Sequence length

    397. 

  397.     my $lf_version;               # Version of LTR finder being parsed

    398. 

  398.     my $lf_trna_db;               # tRNA database used

    399. 

  399.     

    400. 

  400.     my $lf_strand;                # Strand of the LTR

    401. 

  401.     my $lf_span_start;            # Location start

    402. 

  402.     my $lf_span_end;              # Location end

    403. 

  403.     my $lf_length;                # Length

    404. 

  404.     

    405. 

  405.     my $lf_score;                 # Score

    406. 

  406.     my $lf_ltr_similarity;        # Similarity of the LTRs

    407. 

  407.     

    408. 

  408.     # Status strings

    409. 

  409.     my $has_5ltr_tg;                 # TG in 5' END of 5' LTR

    410. 

  410.     my $has_5ltr_ca;                 # CA in 3' END of 5' LTR

    411. 

  411.     my $has_3ltr_tg;                 # TG in 5' END of 3' LTR

    412. 

  412.     my $has_3ltr_ca;                 # CA in 3' END of 3' LTR

    413. 

  413.     my $has_tsr;                     # Has Target Site Replication

    414. 

  414.     my $has_pbs;                     # Has Primer Binding Site

    415. 

  415.     my $has_ppt;                     # Has Poly Purine Tract

    416. 

  416.     my $has_rt;                      # Has Reverse Transcriptase

    417. 

  417.     my $has_in_core;                 # Has Integrase Core

    418. 

  418.     my $has_in_cterm;                # Has Integrase C-term

    419. 

  419.     my $has_rh;                      # Has RNAseH

    420. 

  420.     

    421. 

  421.     my $lf_ltr_id;    # Id number assigned to the LTR retrotransposon

    422. 

  422. 

    423. 

  423.     # LTR COORDINATES

    424. 

  424.     my $lf_5ltr_start;

    425. 

  425.     my $lf_5ltr_end;

    426. 

  426.     my $lf_5ltr_len;

    427. 

  427.     my $lf_3ltr_start;

    428. 

  428.     my $lf_3ltr_end;

    429. 

  429.     my $lf_3ltr_len;

    430. 

  430. 

    431. 

  431.     # TSR COORDINATES

    432. 

  432.     my $lf_5tsr_start;             # Start of the 5' TSR

    433. 

  433.     my $lf_5tsr_end;               # End of the 5' TSR

    434. 

  434.     my $lf_3tsr_start;             # Start of the 3' TSR

    435. 

  435.     my $lf_3tsr_end;               # End of the 3' TSR 

    436. 

  436.     my $lf_tsr_string;             # String of bases in the TSR

    437. 

  437. 

    438. 

  438.     # BOUNDARY SHARPNESS

    439. 

  439.     my $lf_sharp_5;                # Sharpness of 5' Boundary

    440. 

  440.     my $lf_sharp_3;                # Sharpness of 3' Boundary

    441. 

  441.     

    442. 

  442.     # PBS

    443. 

  443.     my $lf_pbs_num_match;          # Number of matched bases in the PBS

    444. 

  444.     my $lf_pbs_aln_len;            # PBS alignment length

    445. 

  445.     my $lf_pbs_start;              # Start of the PBS signal

    446. 

  446.     my $lf_pbs_end;                # End of the PBS signal

    447. 

  447.     my $lf_pbs_trna;               # PBS tRNA type and anti-codon

    448. 

  448. 

    449. 

  449.     # PPT 

    450. 

  450.     my $lf_ppt_num_match;          # Number of matched based in the PPT

    451. 

  451.     my $lf_ppt_aln_len;            # PPT alignment length

    452. 

  452.     my $lf_ppt_start;              # Start of the PPT

    453. 

  453.     my $lf_ppt_end;                # End of the PPT

    454. 

  454.     

    455. 

  455.     #-----------------------------+

    456. 

  456.     # DOMAIN DATA                 |

    457. 

  457.     #-----------------------------+

    458. 

  458.     

    459. 

  459.     # GENERAL DOMAIN VARS

    460. 

  460.     my $lf_domain_dom_start;

    461. 

  461.     my $lf_domain_dom_end;

    462. 

  462.     my $lf_domain_orf_start;

    463. 

  463.     my $lf_domain_orf_end;

    464. 

  464.     my $lf_domain_name;            # Type of the domain

    465. 

  465.     

    466. 

  466.     # INTEGRASE CORE

    467. 

  467.     #my $has_in_core = 0;           # Boolean for has integrase core

    468. 

  468.     my $lf_in_core_dom_start;

    469. 

  469.     my $lf_in_core_dom_end;

    470. 

  470.     my $lf_in_core_orf_start;

    471. 

  471.     my $lf_in_core_orf_end;

    472. 

  472.     

    473. 

  473.     # INTEGRASE C-TERM

    474. 

  474.     #my $has_in_cterm = 0;

    475. 

  475.     my $lf_in_cterm_dom_start;

    476. 

  476.     my $lf_in_cterm_dom_end;

    477. 

  477.     my $lf_in_cterm_orf_start;

    478. 

  478.     my $lf_in_cterm_orf_end;

    479. 

  479. 

    480. 

  480.     # RNASEH

    481. 

  481.     #my $has_rh = 0;

    482. 

  482.     my $lf_rh_dom_start;

    483. 

  483.     my $lf_rh_dom_end;

    484. 

  484.     my $lf_rh_orf_start;

    485. 

  485.     my $lf_rh_orf_end;

    486. 

  486.     

    487. 

  487.     # RT

    488. 

  488.     #my $has_rt = 0;

    489. 

  489.     my $lf_rt_dom_start;

    490. 

  490.     my $lf_rt_dom_end;

    491. 

  491.     my $lf_rt_orf_start;

    492. 

  492.     my $lf_rt_orf_end;

    493. 

  493.     

    494. 

  494. 

    495. 

  495.     #-----------------------------+

    496. 

  496.     # OPEN GFF OUTFILE            |

    497. 

  497.     #-----------------------------+

    498. 

  498.     if ($do_append) {

    499. 

  499. 	open (GFFOUT, ">>$gffout") ||

    500. 

  500. 	    die "ERROR: Can not open gff outfile:\n $gffout\n";

    501. 

  501.     }

    502. 

  502.     else {

    503. 

  503. 	open (GFFOUT,">$gffout") ||

    504. 

  504. 	    die "ERROR: Can not open gff outfile:\n $gffout\n";

    505. 

  505.     }

    506. 

  506. 

    507. 

  507.     #-----------------------------+

    508. 

  508.     # OPEN INPUT FILE             |

    509. 

  509.     #-----------------------------+

    510. 

  510.     open (INFILE, "<$lf_infile") ||

    511. 

  511. 	die "ERROR: Can not open LTR_FINDER result file\n $lf_infile\n";

    512. 

  512. 

    513. 

  513.     while (<INFILE>) {

    514. 

  514. 	chomp;

    515. 

  515.         #    print $_."\n";

    516. 

  516. 	

    517. 

  517. 	

    518. 

  518. 	# CHECK BOOLEANS

    519. 

  519. 	

    520. 

  520. 	

    521. 

  521. 	# 

    522. 

  522. 	if (m/Nothing Header(.*)/) {

    523. 

  523. 	    

    524. 

  524. 	}

    525. 

  525. 	

    526. 

  526. 	#///////////////////////////////////////

    527. 

  527. 	# PAY ATTENTION BELOW THIS MAY BE THE

    528. 

  528. 	# PLACE TO PRINT OUT SAVED GFF DATA

    529. 

  529. 	#\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\

    530. 

  530. 

    531. 

  531. 	# IN NEW REC, GET ID

    532. 

  532. 	elsif (m/^\[(.*)\]/) {

    533. 

  533. 

    534. 

  534. 	    #-----------------------------+

    535. 

  535. 	    # PRINT STORED GFF OUTPUT     |

    536. 

  536. 	    #-----------------------------+

    537. 

  537. 	    unless ($1 == 1 ) {

    538. 

  538. 

    539. 

  539. 		# Two alternatives here

    540. 

  540. 		# keep appending to gff_lout and then print set

    541. 

  541. 		# or print line at a time .. currently printing 

    542. 

  542. 		# a line at a time. JCE 10/02/2007

    543. 

  543. 

    544. 

  544. 		# FULL SPAN

    545. 

  545. 		 $gff_str_out = "$lf_seq_id\t". # Seq ID

    546. 

  546. 		    "$gff_src\t".                # Source

    547. 

  547. 		    "LTR_retrotransposon\t".     # Data type

    548. 

  548. 		    "$lf_span_start\t".          # Start

    549. 

  549. 		    "$lf_span_end\t".            # End

    550. 

  550. 		    "$lf_score\t".               # Score

    551. 

  551. 		    "$lf_strand\t".              # Strand

    552. 

  552. 		    ".\t".                       # Frame

    553. 

  553. 		    "ltr_finder_$lf_ltr_id\n";   # Retro ID

    554. 

  554. 		print STDOUT $gff_str_out;

    555. 

  555. 		print GFFOUT $gff_str_out;

    556. 

  556. 		

    557. 

  557. 

    558. 

  558. 		if ($has_pbs) {

    559. 

  559. 		    $gff_str_out = "$lf_seq_id\t".  # Seq ID

    560. 

  560. 			"$gff_src\t".               # Source

    561. 

  561. 			"primer_binding_site\t".    # Data type

    562. 

  562. 			"$lf_pbs_start\t" .         # Start

    563. 

  563. 			"$lf_pbs_end\t".            # End

    564. 

  564. 			"$lf_score\t".              # Score

    565. 

  565. 			"$lf_strand\t".             # Strand

    566. 

  566. 			".\t".                      # Frame

    567. 

  567. 			"ltr_finder_$lf_ltr_id\n";  # Retro ID

    568. 

  568. 		    print STDOUT $gff_str_out;

    569. 

  569. 		    print GFFOUT $gff_str_out;

    570. 

  570. 		}

    571. 

  571. 

    572. 

  572. 		

    573. 

  573. 		if ($has_ppt) {

    574. 

  574. 		    $gff_str_out = "$lf_seq_id\t".  # Seq ID

    575. 

  575. #		    print STDOUT "$lf_seq_id\t".    # Seq ID

    576. 

  576. 			"$gff_src\t".               # Source

    577. 

  577. 			"RR_tract\t".               # Data type

    578. 

  578. 			"$lf_ppt_start\t".          # Start

    579. 

  579. 			"$lf_ppt_end\t".            # End

    580. 

  580. 			"$lf_score\t".              # Score

    581. 

  581. 			"$lf_strand\t".             # Strand

    582. 

  582. 			".\t".                      # Frame

    583. 

  583. 			"ltr_finder_$lf_ltr_id\n";  # Retro ID

    584. 

  584. 		    print STDOUT $gff_str_out;

    585. 

  585. 		    print GFFOUT $gff_str_out;

    586. 

  586. 		}

    587. 

  587. 

    588. 

  588. 		

    589. 

  589. 		 $gff_str_out = "$lf_seq_id\t".  # Seq ID

    590. 

  590. #		print STDOUT "$lf_seq_id\t".    # Seq ID

    591. 

  591. 		    "$gff_src\t".               # Source

    592. 

  592. 		    "five_prime_LTR\t".         # Data type

    593. 

  593. 		    "$lf_5ltr_start\t".         # Start

    594. 

  594. 		    "$lf_5ltr_end\t".           # End

    595. 

  595. 		    "$lf_score\t".              # Score

    596. 

  596. 		    "$lf_strand\t".             # Strand

    597. 

  597. 		    ".\t".                      # Frame

    598. 

  598. 		    "ltr_finder_$lf_ltr_id\n";  # Retro ID

    599. 

  599. 		 print STDOUT $gff_str_out;

    600. 

  600. 		 print GFFOUT $gff_str_out;

    601. 

  601. 

    602. 

  602. 		 $gff_str_out = "$lf_seq_id\t".  # Seq ID

    603. 

  603. #		print STDOUT "$lf_seq_id\t".    # Seq ID

    604. 

  604. 		    "$gff_src\t".               # Source

    605. 

  605. 		    "three_prime_LTR\t".        # Data type

    606. 

  606. 		    "$lf_3ltr_start\t".         # Start

    607. 

  607. 		    "$lf_3ltr_end\t".           # End

    608. 

  608. 		    "$lf_score\t".              # Score

    609. 

  609. 		    "$lf_strand\t".             # Strand

    610. 

  610. 		    ".\t".                      # Frame

    611. 

  611. 		    "ltr_finder_$lf_ltr_id\n";  # Retro ID

    612. 

  612. 		 print STDOUT $gff_str_out;

    613. 

  613. 		 print GFFOUT $gff_str_out;

    614. 

  614. 

    615. 

  615. 		if ($has_tsr) {

    616. 

  616. 		    

    617. 

  617. 		    $gff_str_out = "$lf_seq_id\t".  # Seq ID

    618. 

  618. #		    print STDOUT "$lf_seq_id\t".     # Seq ID

    619. 

  619. 			"$gff_src\t".              # Source

    620. 

  620. 			"target_site_duplication\t". # Data type

    621. 

  621. 			"$lf_5tsr_start\t".          # Start

    622. 

  622. 			"$lf_5tsr_end\t".            # End

    623. 

  623. 			"$lf_score\t".               # Score

    624. 

  624. 			"$lf_strand\t".              # Strand

    625. 

  625. 			".\t".                       # Frame

    626. 

  626. 			"ltr_finder_$lf_ltr_id\n";   # Retro ID

    627. 

  627. 		    print STDOUT $gff_str_out;

    628. 

  628. 		    print GFFOUT $gff_str_out;	    

    629. 

  629. 

    630. 

  630. 		    $gff_str_out = "$lf_seq_id\t".     # Seq ID

    631. 

  631. 			"$gff_src\t".              # Source

    632. 

  632. 			"target_site_duplication\t". # Data type

    633. 

  633. 			"$lf_3tsr_start\t".          # Start

    634. 

  634. 			"$lf_3tsr_end\t".            # End

    635. 

  635. 			"$lf_score\t".               # Score

    636. 

  636. 			"$lf_strand\t".              # Strand

    637. 

  637. 			".\t".                       # Frame

    638. 

  638. 			"ltr_finder_$lf_ltr_id\n";   # Retro ID

    639. 

  639. 		    print STDOUT $gff_str_out;

    640. 

  640. 		    print GFFOUT $gff_str_out;

    641. 

  641. 		    

    642. 

  642. 		}

    643. 

  643. 

    644. 

  644. 

    645. 

  645. 		# Integrase Core

    646. 

  646. 		if ($has_in_core) {

    647. 

  647. 		    #/////////

    648. 

  648. 		    # NOT SONG

    649. 

  649. 		    #\\\\\\\\\

    650. 

  650. 		    $gff_str_out = "$lf_seq_id\t".     # Seq ID

    651. 

  651. 			"$gff_src\t".              # Source

    652. 

  652. 			"integrase_core_domain\t".  # Data type

    653. 

  653. 			"$lf_in_core_dom_start\t".   # Start

    654. 

  654. 			"$lf_in_core_dom_end\t".     # End

    655. 

  655. 			"$lf_score\t".               # Score

    656. 

  656. 			"$lf_strand\t".              # Strand

    657. 

  657. 			".\t".                       # Frame

    658. 

  658. 			"ltr_finder_$lf_ltr_id\n";   # Retro ID

    659. 

  659. 		    print STDOUT $gff_str_out;

    660. 

  660. 		    print GFFOUT $gff_str_out;

    661. 

  661. 

    662. 

  662. 		    #/////////

    663. 

  663. 		    # NOT SONG

    664. 

  664. 		    #\\\\\\\\\

    665. 

  665. 		    $gff_str_out = "$lf_seq_id\t".     # Seq ID

    666. 

  666. 			"$gff_src\t".              # Source

    667. 

  667. 			"integrase_core_orf\t".      # Data type

    668. 

  668. 			"$lf_in_core_orf_start\t".   # Start

    669. 

  669. 			"$lf_in_core_orf_end\t".     # End

    670. 

  670. 			"$lf_score\t".               # Score

    671. 

  671. 			"$lf_strand\t".              # Strand

    672. 

  672. 			".\t".                       # Frame

    673. 

  673. 			"ltr_finder_$lf_ltr_id\n";   # Retro ID

    674. 

  674. 		    print STDOUT $gff_str_out;

    675. 

  675. 		    print GFFOUT $gff_str_out;

    676. 

  676. 		    

    677. 

  677. 		} # End of has in_core

    678. 

  678. 

    679. 

  679. 

    680. 

  680. 		if ($has_in_cterm) {

    681. 

  681. 

    682. 

  682. 		    #/////////

    683. 

  683. 		    # NOT SONG

    684. 

  684. 		    #\\\\\\\\\

    685. 

  685. 		    $gff_str_out = "$lf_seq_id\t".     # Seq ID

    686. 

  686. 			"$gff_src\t".                # Source

    687. 

  687. 			"integrase_cterm_domain\t".  # Data type

    688. 

  688. 			"$lf_in_cterm_dom_start\t".  # Start

    689. 

  689. 			"$lf_in_cterm_dom_end\t".    # End

    690. 

  690. 			"$lf_score\t".               # Score

    691. 

  691. 			"$lf_strand\t".              # Strand

    692. 

  692. 			".\t".                       # Frame

    693. 

  693. 			"ltr_finder_$lf_ltr_id\n";   # Retro ID

    694. 

  694. 		    print STDOUT $gff_str_out;

    695. 

  695. 		    print GFFOUT $gff_str_out;

    696. 

  696. 

    697. 

  697. 		    $gff_str_out = "$lf_seq_id\t".     # Seq ID

    698. 

  698. 			"$gff_src\t".                # Source

    699. 

  699. 			"integrase_cterm_orf\t".     # Data type

    700. 

  700. 			"$lf_in_cterm_orf_start\t".  # Start

    701. 

  701. 			"$lf_in_cterm_orf_end\t".    # End

    702. 

  702. 			"$lf_score\t".               # Score

    703. 

  703. 			"$lf_strand\t".              # Strand

    704. 

  704. 			".\t".                       # Frame

    705. 

  705. 			"ltr_finder_$lf_ltr_id\n";   # Retro ID

    706. 

  706. 		    print STDOUT $gff_str_out;

    707. 

  707. 		    print GFFOUT $gff_str_out;

    708. 

  708. 		    

    709. 

  709. 		} # End of has_in_cterm

    710. 

  710. 

    711. 

  711. 		if ($has_rh) {

    712. 

  712. 

    713. 

  713. 		    #/////////

    714. 

  714. 		    # NOT SONG

    715. 

  715. 		    #\\\\\\\\\

    716. 

  716. 		    $gff_str_out = "$lf_seq_id\t".     # Seq ID

    717. 

  717. 			"$gff_src\t".                # Source

    718. 

  718. 			"rnaseh_domain\t".           # Data type

    719. 

  719. 			"$lf_rh_dom_start\t".        # Start

    720. 

  720. 			"$lf_rh_dom_end\t".          # End

    721. 

  721. 			"$lf_score\t".               # Score

    722. 

  722. 			"$lf_strand\t".              # Strand

    723. 

  723. 			".\t".                       # Frame

    724. 

  724. 			"ltr_finder_$lf_ltr_id\n";   # Retro ID

    725. 

  725. 		    print STDOUT $gff_str_out;

    726. 

  726. 		    print GFFOUT $gff_str_out;

    727. 

  727. 

    728. 

  728. 		    $gff_str_out = "$lf_seq_id\t".     # Seq ID

    729. 

  729. 			"$gff_src\t".                # Source

    730. 

  730. 			"rnaseh_orf\t".              # Data type

    731. 

  731. 			"$lf_rh_orf_start\t".        # Start

    732. 

  732. 			"$lf_rh_orf_end\t".          # End

    733. 

  733. 			"$lf_score\t".               # Score

    734. 

  734. 			"$lf_strand\t".              # Strand

    735. 

  735. 			".\t".                       # Frame

    736. 

  736. 			"ltr_finder_$lf_ltr_id\n";   # Retro ID

    737. 

  737. 		    print STDOUT $gff_str_out;

    738. 

  738. 		    print GFFOUT $gff_str_out;

    739. 

  739. 		    

    740. 

  740. 		}

    741. 

  741. 

    742. 

  742. 		if ($has_rt) {

    743. 

  743. 

    744. 

  744. 		    #/////////

    745. 

  745. 		    # NOT SONG

    746. 

  746. 		    #\\\\\\\\\

    747. 

  747. 		    $gff_str_out = "$lf_seq_id\t".     # Seq ID

    748. 

  748. 			"$gff_src\t".                # Source

    749. 

  749. 			"rt_domain\t".               # Data type

    750. 

  750. 			"$lf_rt_dom_start\t".        # Start

    751. 

  751. 			"$lf_rt_dom_end\t".          # End

    752. 

  752. 			"$lf_score\t".               # Score

    753. 

  753. 			"$lf_strand\t".              # Strand

    754. 

  754. 			".\t".                       # Frame

    755. 

  755. 			"ltr_finder_$lf_ltr_id\n";   # Retro ID

    756. 

  756. 		    print STDOUT $gff_str_out;

    757. 

  757. 		    print GFFOUT $gff_str_out;

    758. 

  758. 

    759. 

  759. 		    $gff_str_out = "$lf_seq_id\t".     # Seq ID

    760. 

  760. 			"$gff_src\t".                # Source

    761. 

  761. 			"rt_orf\t".                  # Data type

    762. 

  762. 			"$lf_rt_orf_start\t".        # Start

    763. 

  763. 			"$lf_rt_orf_end\t".          # End

    764. 

  764. 			"$lf_score\t".               # Score

    765. 

  765. 			"$lf_strand\t".              # Strand

    766. 

  766. 			".\t".                       # Frame

    767. 

  767. 			"ltr_finder_$lf_ltr_id\n";   # Retro ID

    768. 

  768. 		    print STDOUT $gff_str_out;

    769. 

  769. 		    print GFFOUT $gff_str_out;

    770. 

  770. 

    771. 

  771. 		} # End of has_reverse_transcriptase

    772. 

  772. 

    773. 

  773. 	    } # End of unless this is the first record

    774. 

  774. 

    775. 

  775. 

    776. 

  776. 	    #-----------------------------+

    777. 

  777. 	    # RESET VARS TO NULL          |

    778. 

  778. 	    #-----------------------------+

    779. 

  779. 	    # May not need to reset vars since existence of the vars

    780. 

  780. 	    # is designated by the do_* variables.

    781. 

  781. 	    

    782. 

  782. 	    #-----------------------------+

    783. 

  783. 	    # LOAD ID VAR                 |

    784. 

  784. 	    #-----------------------------+

    785. 

  785. 	    $lf_ltr_id = $1;

    786. 

  786. 

    787. 

  787. 	}

    788. 

  788. 	

    789. 

  789. 	# SEQ ID AND LENGTH

    790. 

  790. 	elsif (m/>Sequence: (.*) Len:(.*)/){

    791. 

  791. 	    $lf_seq_id = $1;

    792. 

  792. 	    $lf_seq_len = $2;

    793. 

  793. 	}

    794. 

  794. 	

    795. 

  795. 	# SPAN LOCATION, LENGTH, AND STRAND

    796. 

  796. 	elsif (m/^Location : (\d*) - (\d*) Len: (\d*) Strand:(.)/){

    797. 

  797. 	    $lf_span_start = $1;

    798. 

  798. 	    $lf_span_end = $2;

    799. 

  799. 	    $lf_length = $3;

    800. 

  800. 	    $lf_strand = $4;

    801. 

  801. 	}

    802. 

  802. 	

    803. 

  803. 	# SCORE SIMILARITY

    804. 

  804. 	elsif (m/^Score    : (.*) \[LTR region similarity:(.*)\]/){

    805. 

  805. 	    $lf_score = $1;

    806. 

  806. 	    $lf_ltr_similarity = $2;

    807. 

  807. 	}

    808. 

  808. 	

    809. 

  809. 	# STATUS SET

    810. 

  810. 	elsif (m/^Status   : (\d)(\d)(\d)(\d)(\d)(\d)(\d)(\d)(\d)(\d)(\d)/){

    811. 

  811. 	    # Since this is a binary string, it can be split as digits

    812. 

  812. 	    # and used to load the $has_* booleans

    813. 

  813. 	    $has_5ltr_tg = $1;

    814. 

  814. 	    $has_5ltr_ca = $2;

    815. 

  815. 	    $has_3ltr_tg = $3;

    816. 

  816. 	    $has_3ltr_ca = $4;

    817. 

  817. 	    $has_tsr = $5;

    818. 

  818. 	    $has_pbs = $6;

    819. 

  819. 	    $has_ppt = $7;

    820. 

  820. 	    $has_rt = $8;

    821. 

  821. 	    $has_in_core = $9;

    822. 

  822. 	    $has_in_cterm = $10;

    823. 

  823. 	    $has_rh = $11;

    824. 

  824. 	}

    825. 

  825. 	

    826. 

  826. 	# 5' LTR

    827. 

  827. 	elsif (m/^5\'-LTR   : (\d*) - (\d*) Len: (\d*)/){

    828. 

  828. 	    $lf_5ltr_start = $1;

    829. 

  829. 	    $lf_5ltr_end = $2;

    830. 

  830. 	    $lf_5ltr_len = $3;

    831. 

  831. 	}

    832. 

  832. 	

    833. 

  833. 	# 3' LTR

    834. 

  834. 	elsif (m/^3\'-LTR   : (\d*) - (\d*) Len: (\d*)/){

    835. 

  835. 	    $lf_3ltr_start = $1;

    836. 

  836. 	    $lf_3ltr_end = $2;

    837. 

  837. 	    $lf_3ltr_len = $3;

    838. 

  838. 	}

    839. 

  839. 	

    840. 

  840.     # TARGET SITE REPLICATION

    841. 

  841. 	elsif (m/TSR      : (\d*) - (\d*) , (\d*) - (\d*) \[(.*)\]/){

    842. 

  842. 	    $lf_5tsr_start = $1;

    843. 

  843. 	    $lf_5tsr_end = $2;

    844. 

  844. 	    $lf_3tsr_start = $3;

    845. 

  845. 	    $lf_3tsr_end = $4;

    846. 

  846. 	    $lf_tsr_string = $5;

    847. 

  847. 	}

    848. 

  848. 	

    849. 

  849. 	# SHARPNESS METRIC

    850. 

  850. 	elsif (m/^Sharpness: (.*),(.*)/){

    851. 

  851. 	    $lf_sharp_5 = $1;

    852. 

  852. 	    $lf_sharp_3 = $2;

    853. 

  853. 	}

    854. 

  854. 	

    855. 

  855. 	# PBS

    856. 

  856. 	elsif (m/PBS   : \[(\d*)\/(\d*)\] (\d*) - (\d*) \((.*)\)/) {

    857. 

  857. 	    $lf_pbs_num_match = $1;

    858. 

  858. 	    $lf_pbs_aln_len = $2;

    859. 

  859. 	    $lf_pbs_start = $3;

    860. 

  860. 	    $lf_pbs_end = $4;

    861. 

  861. 	    $lf_pbs_trna = $5;

    862. 

  862. 	}

    863. 

  863. 	

    864. 

  864. 	# PPT

    865. 

  865. 	elsif (m/PPT   : \[(\d*)\/(\d*)\] (\d*) - (\d*)/) {

    866. 

  866. 	    $lf_ppt_num_match = $1;

    867. 

  867. 	    $lf_ppt_aln_len = $2;

    868. 

  868. 	    $lf_ppt_start = $3;

    869. 

  869. 	    $lf_ppt_end = $4;

    870. 

  870. 	}

    871. 

  871. 	

    872. 

  872. 	# PROTEIN DOMAINS

    873. 

  873. 	# This will need to be modified and checked after another run

    874. 

  874. 	# using ps_scan to get the additional domains

    875. 

  875. 	#

    876. 

  876. 	#Domain: 56796 - 57326 [possible ORF:56259-59144, (IN (core))]

    877. 

  877. 	elsif (m/Domain: (\d*) - (\d*) \[possible ORF:(\d*)-(\d*), \((.*)\)\]/) {

    878. 

  878. 	    

    879. 

  879. 	    $lf_domain_dom_start = $1;

    880. 

  880. 	    $lf_domain_dom_end = $2;

    881. 

  881. 	    $lf_domain_orf_start = $3;

    882. 

  882. 	    $lf_domain_orf_end = $4;

    883. 

  883. 	    $lf_domain_name = $5;

    884. 

  884. 	    

    885. 

  885. 	    # Temp while I work with this data

    886. 

  886. 	    #print "DOMAIN:".$lf_domain_name."\n";

    887. 

  887. 	    

    888. 

  888. 	    if ($lf_domain_name =~ 'IN \(core\)') {

    889. 

  889. 		

    890. 

  890. 		$lf_in_core_dom_start = $lf_domain_dom_start;

    891. 

  891. 		$lf_in_core_dom_end = $lf_domain_dom_end;

    892. 

  892. 		$lf_in_core_orf_start = $lf_domain_orf_start;

    893. 

  893. 		$lf_in_core_orf_end = $lf_domain_orf_end;

    894. 

  894. 		

    895. 

  895. 		# Temp while debug

    896. 

  896. 		# This is to check the regexp vars can be fetched here

    897. 

  897. 		#print "\tDom Start: $lf_in_core_dom_start\n";

    898. 

  898. 		#print "\tDom End:   $lf_in_core_dom_end\n";

    899. 

  899. 		#print "\tOrf Start: $lf_in_core_orf_start\n";

    900. 

  900. 		#print "\tOrf End:   $lf_in_core_orf_end\n";

    901. 

  901. 		

    902. 

  902. 	    }

    903. 

  903. 	    elsif ($lf_domain_name =~ 'IN \(c-term\)') {

    904. 

  904. 		$lf_in_cterm_dom_start = $lf_domain_dom_start;

    905. 

  905. 		$lf_in_cterm_dom_end = $lf_domain_dom_end;

    906. 

  906. 		$lf_in_cterm_orf_start = $lf_domain_orf_start;

    907. 

  907. 		$lf_in_cterm_orf_end = $lf_domain_orf_end;

    908. 

  908. 	    }

    909. 

  909. 	    elsif ($lf_domain_name =~ 'RH') {

    910. 

  910. 		$lf_rh_dom_start = $lf_domain_dom_start;

    911. 

  911. 		$lf_rh_dom_end = $lf_domain_dom_end;

    912. 

  912. 		$lf_rh_orf_start = $lf_domain_orf_start;

    913. 

  913. 		$lf_rh_orf_end = $lf_domain_orf_end;

    914. 

  914. 	    }

    915. 

  915. 	    elsif ($lf_domain_name =~ 'RT') {

    916. 

  916. 		

    917. 

  917. 		$lf_rt_dom_start = $lf_domain_dom_start;

    918. 

  918. 		$lf_rt_dom_end = $lf_domain_dom_end;

    919. 

  919. 		$lf_rt_orf_start = $lf_domain_orf_start;

    920. 

  920. 		$lf_rt_orf_end = $lf_domain_orf_end;  

    921. 

  921. 		

    922. 

  922. 	    }

    923. 

  923. 	    else {

    924. 

  924. 		print "\a";

    925. 

  925. 		print STDERR "Unknown domain type: $lf_domain_name\n";

    926. 

  926. 	    }

    927. 

  927. 	    

    928. 

  928. 	    

    929. 

  929. 	    

    930. 

  930. 	} # End of elsif Domain

    931. 

  931. 	

    932. 

  932. 	#-----------------------------+

    933. 

  933. 	# FILE HEADER INFORMATION     |

    934. 

  934. 	#-----------------------------+

    935. 

  935. 	

    936. 

  936. 	# PROGRAM NAME

    937. 

  937. 	elsif (m/^Program    : (.*)/) {

    938. 

  938. 	    $lf_prog_name = $1;

    939. 

  939. 	}

    940. 

  940. 	

    941. 

  941. 	# PROGRAM VERSION

    942. 

  942. 	elsif (m/^Version    : (.*)/) {

    943. 

  943. 	    $lf_version = $1;

    944. 

  944. 	}

    945. 

  945. 	

    946. 

  946.     }

    947. 

  947.     

    948. 

  948.     close INFILE;

    949. 

  949.     

    950. 

  950.     #-----------------------------+

    951. 

  951.     # PRINT LAST GFFOUT           |

    952. 

  952.     #-----------------------------+

    953. 

  953.     

    954. 

  954.     # FULL SPAN

    955. 

  955.     $gff_str_out = "$lf_seq_id\t". # Seq ID

    956. 

  956. 	"$gff_src\t".                # Source

    957. 

  957. 	"LTR_retrotransposon\t".     # Data type

    958. 

  958. 	"$lf_span_start\t".          # Start

    959. 

  959. 	"$lf_span_end\t".            # End

    960. 

  960. 	"$lf_score\t".               # Score

    961. 

  961. 	"$lf_strand\t".              # Strand

    962. 

  962. 	".\t".                       # Frame

    963. 

  963. 	"ltr_finder_$lf_ltr_id\n";   # Retro ID

    964. 

  964.     print STDOUT $gff_str_out;

    965. 

  965.     print GFFOUT $gff_str_out;

    966. 

  966.     

    967. 

  967.     

    968. 

  968.     if ($has_pbs) {

    969. 

  969. 	$gff_str_out = "$lf_seq_id\t".  # Seq ID

    970. 

  970. 	    "$gff_src\t".               # Source

    971. 

  971. 	    "primer_binding_site\t".    # Data type

    972. 

  972. 	    "$lf_pbs_start\t" .         # Start

    973. 

  973. 	    "$lf_pbs_end\t".            # End

    974. 

  974. 	    "$lf_score\t".              # Score

    975. 

  975. 	    "$lf_strand\t".             # Strand

    976. 

  976. 	    ".\t".                      # Frame

    977. 

  977. 	    "ltr_finder_$lf_ltr_id\n";  # Retro ID

    978. 

  978. 	print STDOUT $gff_str_out;

    979. 

  979. 	print GFFOUT $gff_str_out;

    980. 

  980.     }

    981. 

  981.     

    982. 

  982.     

    983. 

  983.     if ($has_ppt) {

    984. 

  984. 	$gff_str_out = "$lf_seq_id\t".  # Seq ID

    985. 

  985. #		    print STDOUT "$lf_seq_id\t".    # Seq ID

    986. 

  986. 	    "$gff_src\t".               # Source

    987. 

  987. 	    "RR_tract\t".               # Data type

    988. 

  988. 	    "$lf_ppt_start\t".          # Start

    989. 

  989. 	    "$lf_ppt_end\t".            # End

    990. 

  990. 	    "$lf_score\t".              # Score

    991. 

  991. 	    "$lf_strand\t".             # Strand

    992. 

  992. 	    ".\t".                      # Frame

    993. 

  993. 	    "ltr_finder_$lf_ltr_id\n";  # Retro ID

    994. 

  994. 	print STDOUT $gff_str_out;

    995. 

  995. 	print GFFOUT $gff_str_out;

    996. 

  996.     }

    997. 

  997.     

    998. 

  998.     

    999. 

  999.     $gff_str_out = "$lf_seq_id\t".  # Seq ID

    1000. 

  1000. #		print STDOUT "$lf_seq_id\t".    # Seq ID

    1001. 

  1001. 	"$gff_src\t".               # Source

    1002. 

  1002. 	"five_prime_LTR\t".         # Data type

    1003. 

  1003. 	"$lf_5ltr_start\t".         # Start

    1004. 

  1004. 	"$lf_5ltr_end\t".           # End

    1005. 

  1005. 	"$lf_score\t".              # Score

    1006. 

  1006. 	"$lf_strand\t".             # Strand

    1007. 

  1007. 	".\t".                      # Frame

    1008. 

  1008. 	"ltr_finder_$lf_ltr_id\n";  # Retro ID

    1009. 

  1009.     print STDOUT $gff_str_out;

    1010. 

  1010.     print GFFOUT $gff_str_out;

    1011. 

  1011.     

    1012. 

  1012. 

    1013. 

  1013.     # Getting an error beow

    1014. 

  1014.     $gff_str_out = "$lf_seq_id\t".  # Seq ID

    1015. 

  1015. #		print STDOUT "$lf_seq_id\t".    # Seq ID

    1016. 

  1016. 	"$gff_src\t".               # Source

    1017. 

  1017. 	"three_prime_LTR\t".        # Data type

    1018. 

  1018. 	"$lf_3ltr_start\t".         # Start

    1019. 

  1019. 	"$lf_3ltr_end\t".           # End

    1020. 

  1020. 	"$lf_score\t".              # Score

    1021. 

  1021. 	"$lf_strand\t".             # Strand

    1022. 

  1022. 	".\t".                      # Frame

    1023. 

  1023. 	"ltr_finder_$lf_ltr_id\n";  # Retro ID

    1024. 

  1024.     print STDOUT $gff_str_out;

    1025. 

  1025.     print GFFOUT $gff_str_out;

    1026. 

  1026.     

    1027. 

  1027.     if ($has_tsr) {

    1028. 

  1028. 	

    1029. 

  1029. 	$gff_str_out = "$lf_seq_id\t".   # Seq ID

    1030. 

  1030. #		    print STDOUT "$lf_seq_id\t".     # Seq ID

    1031. 

  1031. 	    "$gff_src\t".                # Source

    1032. 

  1032. 	    "target_site_duplication\t". # Data type

    1033. 

  1033. 	    "$lf_5tsr_start\t".          # Start

    1034. 

  1034. 	    "$lf_5tsr_end\t".            # End

    1035. 

  1035. 	    "$lf_score\t".               # Score

    1036. 

  1036. 	    "$lf_strand\t".              # Strand

    1037. 

  1037. 	    ".\t".                       # Frame

    1038. 

  1038. 	    "ltr_finder_$lf_ltr_id\n";   # Retro ID

    1039. 

  1039. 	print STDOUT $gff_str_out;

    1040. 

  1040. 	print GFFOUT $gff_str_out;	    

    1041. 

  1041. 	

    1042. 

  1042. 	$gff_str_out = "$lf_seq_id\t".   # Seq ID

    1043. 

  1043. 	    "$gff_src\t".                # Source

    1044. 

  1044. 	    "target_site_duplication\t". # Data type

    1045. 

  1045. 	    "$lf_3tsr_start\t".          # Start

    1046. 

  1046. 	    "$lf_3tsr_end\t".            # End

    1047. 

  1047. 	    "$lf_score\t".               # Score

    1048. 

  1048. 	    "$lf_strand\t".              # Strand

    1049. 

  1049. 	    ".\t".                       # Frame

    1050. 

  1050. 	    "ltr_finder_$lf_ltr_id\n";   # Retro ID

    1051. 

  1051. 	print STDOUT $gff_str_out;

    1052. 

  1052. 	print GFFOUT $gff_str_out;

    1053. 

  1053. 	

    1054. 

  1054.     }

    1055. 

  1055.     

    1056. 

  1056.     

    1057. 

  1057.     # Integrase Core

    1058. 

  1058.     if ($has_in_core) {

    1059. 

  1059. 	#/////////

    1060. 

  1060. 	# NOT SONG

    1061. 

  1061. 	#\\\\\\\\\

    1062. 

  1062. 	$gff_str_out = "$lf_seq_id\t".     # Seq ID

    1063. 

  1063. 	    "$gff_src\t".              # Source

    1064. 

  1064. 	    "integrase_core_domain\t".  # Data type

    1065. 

  1065. 	    "$lf_in_core_dom_start\t".   # Start

    1066. 

  1066. 	    "$lf_in_core_dom_end\t".     # End

    1067. 

  1067. 	    "$lf_score\t".               # Score

    1068. 

  1068. 	    "$lf_strand\t".              # Strand

    1069. 

  1069. 	    ".\t".                       # Frame

    1070. 

  1070. 	    "ltr_finder_$lf_ltr_id\n";   # Retro ID

    1071. 

  1071. 	print STDOUT $gff_str_out;

    1072. 

  1072. 	print GFFOUT $gff_str_out;

    1073. 

  1073. 	

    1074. 

  1074. 	#/////////

    1075. 

  1075. 	# NOT SONG

    1076. 

  1076. 	#\\\\\\\\\

    1077. 

  1077. 	$gff_str_out = "$lf_seq_id\t".     # Seq ID

    1078. 

  1078. 	    "$gff_src\t".              # Source

    1079. 

  1079. 	    "integrase_core_orf\t".      # Data type

    1080. 

  1080. 	    "$lf_in_core_orf_start\t".   # Start

    1081. 

  1081. 	    "$lf_in_core_orf_end\t".     # End

    1082. 

  1082. 	    "$lf_score\t".               # Score

    1083. 

  1083. 	    "$lf_strand\t".              # Strand

    1084. 

  1084. 	    ".\t".                       # Frame

    1085. 

  1085. 	    "ltr_finder_$lf_ltr_id\n";   # Retro ID

    1086. 

  1086. 	print STDOUT $gff_str_out;

    1087. 

  1087. 	print GFFOUT $gff_str_out;

    1088. 

  1088. 	

    1089. 

  1089.     } # End of has in_core

    1090. 

  1090.     

    1091. 

  1091.     

    1092. 

  1092.     if ($has_in_cterm) {

    1093. 

  1093. 	

    1094. 

  1094. 	#/////////

    1095. 

  1095. 	# NOT SONG

    1096. 

  1096. 	#\\\\\\\\\

    1097. 

  1097. 	$gff_str_out = "$lf_seq_id\t".     # Seq ID

    1098. 

  1098. 	    "$gff_src\t".                # Source

    1099. 

  1099. 	    "integrase_cterm_domain\t".  # Data type

    1100. 

  1100. 	    "$lf_in_cterm_dom_start\t".  # Start

    1101. 

  1101. 	    "$lf_in_cterm_dom_end\t".    # End

    1102. 

  1102. 	    "$lf_score\t".               # Score

    1103. 

  1103. 	    "$lf_strand\t".              # Strand

    1104. 

  1104. 	    ".\t".                       # Frame

    1105. 

  1105. 	    "ltr_finder_$lf_ltr_id\n";   # Retro ID

    1106. 

  1106. 	print STDOUT $gff_str_out;

    1107. 

  1107. 	print GFFOUT $gff_str_out;

    1108. 

  1108. 	

    1109. 

  1109. 	$gff_str_out = "$lf_seq_id\t".     # Seq ID

    1110. 

  1110. 	    "$gff_src\t".                # Source

    1111. 

  1111. 	    "integrase_cterm_orf\t".     # Data type

    1112. 

  1112. 	    "$lf_in_cterm_orf_start\t".  # Start

    1113. 

  1113. 	    "$lf_in_cterm_orf_end\t".    # End

    1114. 

  1114. 	    "$lf_score\t".               # Score

    1115. 

  1115. 	    "$lf_strand\t".              # Strand

    1116. 

  1116. 	    ".\t".                       # Frame

    1117. 

  1117. 	    "ltr_finder_$lf_ltr_id\n";   # Retro ID

    1118. 

  1118. 	print STDOUT $gff_str_out;

    1119. 

  1119. 	print GFFOUT $gff_str_out;

    1120. 

  1120. 	

    1121. 

  1121.     } # End of has_in_cterm

    1122. 

  1122.     

    1123. 

  1123.     if ($has_rh) {

    1124. 

  1124. 	

    1125. 

  1125. 	#/////////

    1126. 

  1126. 	# NOT SONG

    1127. 

  1127. 	#\\\\\\\\\

    1128. 

  1128. 	$gff_str_out = "$lf_seq_id\t".     # Seq ID

    1129. 

  1129. 	    "$gff_src\t".                # Source

    1130. 

  1130. 	    "rnaseh_domain\t".           # Data type

    1131. 

  1131. 	    "$lf_rh_dom_start\t".        # Start

    1132. 

  1132. 	    "$lf_rh_dom_end\t".          # End

    1133. 

  1133. 	    "$lf_score\t".               # Score

    1134. 

  1134. 	    "$lf_strand\t".              # Strand

    1135. 

  1135. 	    ".\t".                       # Frame

    1136. 

  1136. 	    "ltr_finder_$lf_ltr_id\n";   # Retro ID

    1137. 

  1137. 	print STDOUT $gff_str_out;

    1138. 

  1138. 	print GFFOUT $gff_str_out;

    1139. 

  1139. 	

    1140. 

  1140. 	$gff_str_out = "$lf_seq_id\t".     # Seq ID

    1141. 

  1141. 	    "$gff_src\t".                # Source

    1142. 

  1142. 	    "rnaseh_orf\t".              # Data type

    1143. 

  1143. 	    "$lf_rh_orf_start\t".        # Start

    1144. 

  1144. 	    "$lf_rh_orf_end\t".          # End

    1145. 

  1145. 	    "$lf_score\t".               # Score

    1146. 

  1146. 	    "$lf_strand\t".              # Strand

    1147. 

  1147. 	    ".\t".                       # Frame

    1148. 

  1148. 	    "ltr_finder_$lf_ltr_id\n";   # Retro ID

    1149. 

  1149. 	print STDOUT $gff_str_out;

    1150. 

  1150. 	print GFFOUT $gff_str_out;

    1151. 

  1151. 	

    1152. 

  1152.     }

    1153. 

  1153.     

    1154. 

  1154.     if ($has_rt) {

    1155. 

  1155. 	

    1156. 

  1156. 	#/////////

    1157. 

  1157. 	# NOT SONG

    1158. 

  1158. 	#\\\\\\\\\

    1159. 

  1159. 	$gff_str_out = "$lf_seq_id\t".     # Seq ID

    1160. 

  1160. 	    "$gff_src\t".                # Source

    1161. 

  1161. 	    "rt_domain\t".               # Data type

    1162. 

  1162. 	    "$lf_rt_dom_start\t".        # Start

    1163. 

  1163. 	    "$lf_rt_dom_end\t".          # End

    1164. 

  1164. 	    "$lf_score\t".               # Score

    1165. 

  1165. 	    "$lf_strand\t".              # Strand

    1166. 

  1166. 	    ".\t".                       # Frame

    1167. 

  1167. 	    "ltr_finder_$lf_ltr_id\n";   # Retro ID

    1168. 

  1168. 	print STDOUT $gff_str_out;

    1169. 

  1169. 	print GFFOUT $gff_str_out;

    1170. 

  1170. 	

    1171. 

  1171. 	$gff_str_out = "$lf_seq_id\t".     # Seq ID

    1172. 

  1172. 	    "$gff_src\t".                # Source

    1173. 

  1173. 	    "rt_orf\t".                  # Data type

    1174. 

  1174. 	    "$lf_rt_orf_start\t".        # Start

    1175. 

  1175. 	    "$lf_rt_orf_end\t".          # End

    1176. 

  1176. 	    "$lf_score\t".               # Score

    1177. 

  1177. 	    "$lf_strand\t".              # Strand

    1178. 

  1178. 	    ".\t".                       # Frame

    1179. 

  1179. 	    "ltr_finder_$lf_ltr_id\n";   # Retro ID

    1180. 

  1180. 	print STDOUT $gff_str_out;

    1181. 

  1181. 	print GFFOUT $gff_str_out;

    1182. 

  1182. 	

    1183. 

  1183.     } # End of has_reverse_transcriptase

    1184. 

  1184.     

    1185. 

  1185.     

    1186. 

  1186.     close GFFOUT;

    1187. 

  1187. 

    1188. 

  1188. } # End of ltrfinder2gff subfunction

    1189. 

  1189. 

    1190. 

  1190. 

    1191. 

  1191. =head1 NAME

    1192. 

  1192. 

    1193. 

  1193. Name.pl - Short program description. 

    1194. 

  1194. 

    1195. 

  1195. =head1 VERSION

    1196. 

  1196. 

    1197. 

  1197. This documentation refers to program version 0.1

    1198. 

  1198. 

    1199. 

  1199. =head1 SYNOPSIS

    1200. 

  1200. 

    1201. 

  1201.   USAGE:

    1202. 

  1202.     Name.pl -i InFile -o OutFile

    1203. 

  1203. 

    1204. 

  1204.     --infile        # Path to the input file

    1205. 

  1205.     --outfie        # Path to the output file

    1206. 

  1206. 

    1207. 

  1207. =head1 DESCRIPTION

    1208. 

  1208. 

    1209. 

  1209. This is what the program does

    1210. 

  1210. 

    1211. 

  1211. =head1 COMMAND LINE ARGUMENTS

    1212. 

  1212. 

    1213. 

  1213. =head 2 Required Arguments

    1214. 

  1214. 

    1215. 

  1215. =over 2

    1216. 

  1216. 

    1217. 

  1217. =item -i,--infile

    1218. 

  1218. 

    1219. 

  1219. Path of the input file.

    1220. 

  1220. 

    1221. 

  1221. =item -o,--outfile

    1222. 

  1222. 

    1223. 

  1223. Path of the output file.

    1224. 

  1224. 

    1225. 

  1225. =back

    1226. 

  1226. 

    1227. 

  1227. =head1 Additional Options

    1228. 

  1228. 

    1229. 

  1229. =over

    1230. 

  1230. 

    1231. 

  1231. =over 2

    1232. 

  1232. 

    1233. 

  1233. =item --usage

    1234. 

  1234. 

    1235. 

  1235. Short overview of how to use program from command line.

    1236. 

  1236. 

    1237. 

  1237. =item --help

    1238. 

  1238. 

    1239. 

  1239. Show program usage with summary of options.

    1240. 

  1240. 

    1241. 

  1241. =item --version

    1242. 

  1242. 

    1243. 

  1243. Show program version.

    1244. 

  1244. 

    1245. 

  1245. =item --man

    1246. 

  1246. 

    1247. 

  1247. Show the full program manual. This uses the perldoc command to print the 

    1248. 

  1248. POD documentation for the program.

    1249. 

  1249. 

    1250. 

  1250. =item -q,--quiet

    1251. 

  1251. 

    1252. 

  1252. Run the program with minimal output.

    1253. 

  1253. 

    1254. 

  1254. =back

    1255. 

  1255. 

    1256. 

  1256. =head1 DIAGNOSTICS

    1257. 

  1257. 

    1258. 

  1258. The list of error messages that can be generated,

    1259. 

  1259. explanation of the problem

    1260. 

  1260. one or more causes

    1261. 

  1261. suggested remedies

    1262. 

  1262. list exit status associated with each error

    1263. 

  1263. 

    1264. 

  1264. =head1 CONFIGURATION AND ENVIRONMENT

    1265. 

  1265. 

    1266. 

  1266. Names and locations of config files

    1267. 

  1267. environmental variables

    1268. 

  1268. or properties that can be set.

    1269. 

  1269. 

    1270. 

  1270. =head1 DEPENDENCIES

    1271. 

  1271. 

    1272. 

  1272. Other modules or software that the program is dependent on.

    1273. 

  1273. 

    1274. 

  1274. =head1 BUGS AND LIMITATIONS

    1275. 

  1275. 

    1276. 

  1276. Any known bugs and limitations will be listed here.

    1277. 

  1277. 

    1278. 

  1278. =head1 LICENSE

    1279. 

  1279. 

    1280. 

  1280. GNU LESSER GENERAL PUBLIC LICENSE

    1281. 

  1281. 

    1282. 

  1282. http://www.gnu.org/licenses/lgpl.html

    1283. 

  1283. 

    1284. 

  1284. =head1 AUTHOR

    1285. 

  1285. 

    1286. 

  1286. James C. Estill E<lt>JamesEstill at gmail.comE<gt>

    1287. 

  1287. 

    1288. 

  1288. =head1 HISTORY

    1289. 

  1289. 

    1290. 

  1290. STARTED: 10/02/2007

    1291. 

  1291. 

    1292. 

  1292. UPDATED: 10/02/2007

    1293. 

  1293. 

    1294. 

  1294. VERSION: $Rev$

    1295. 

  1295. 

    1296. 

  1296. =cut

    1297. 

  1297. 

    1298. 

  1298. #-----------------------------------------------------------+

    1299. 

  1299. # HISTORY                                                   |

    1300. 

  1300. #-----------------------------------------------------------+

    1301. 

  1301. #

    1302. 

  1302. # 10/02/2007

    1303. 

  1303. # - Started program from general template

    1304. 

  1304. # - Added the ltrfinder2gff subfunction from the 

    1305. 

  1305. #   cnv_ltrfinder2gff program.

    1306. 

  1306.