Mercurial > repos > greg > resize_coordinate_window
changeset 0:d64206d13298 draft default tip
Uploaded
| author | greg |
|---|---|
| date | Wed, 06 Jan 2016 15:15:56 -0500 |
| parents | |
| children | |
| files | resize_coordinate_window.pl resize_coordinate_window.xml test-data/input.gff test-data/output.gff tool_dependencies.xml |
| diffstat | 5 files changed, 272 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/resize_coordinate_window.pl Wed Jan 06 15:15:56 2016 -0500 @@ -0,0 +1,27 @@ +#! /usr/bin/perl + +my($input, $SIZE) = @ARGV; +open(IN, "<$input") or die "Can't open $input for reading!\n"; + +#chr1 genetrack . 123950 123970 22 + . stddev=0.0 +#chr1 genetrack . 565745 565765 12 + . stddev=0.0 +#chr1 genetrack . 565793 565813 44 + . stddev=0.298065387468 + +$line = ""; +while($line = <IN>) { + chomp($line); + @array = split(/\t/, $line); + + $CENTER = int(($array[3] + $array[4]) / 2); + if(($array[4] - $array[3]) % 2 != 0 || $array[6] eq "-") { $CENTER++; } + $START = $CENTER - ($SIZE / 2); + $STOP = $CENTER + (($SIZE / 2) - 1); + + if($START < 1) { print STDERR "Error:\t$line\nRequested expansion places region beyond chromosome bounds!!!\n"; } + else { + print "$array[0]\t$array[1]\t$array[2]\t$START\t$STOP"; + for($x = 5; $x <= $#array; $x++) { print "\t$array[$x]"; } + print "\n"; + } +} +close IN;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/resize_coordinate_window.xml Wed Jan 06 15:15:56 2016 -0500 @@ -0,0 +1,39 @@ +<tool id="resize_coordinate_window" name="Resize coordinate window" version="1.0.0"> + <description>of GFF data</description> + <requirements> + <requirement type="package" version="5.18.1">perl</requirement> + </requirements> + <command>perl $__tool_directory__/resize_coordinate_window.pl "$input" $window "$output"</command> + <inputs> + <param name="input" type="data" format="gff" label="Gff file" /> + <param name="window" type="integer" value="0" label="Window size in base pairs" /> + </inputs> + <outputs> + <data name="output" format="gff" /> + </outputs> + <tests> + <test> + <param name="input" value="input.gff" ftype="gff" /> + <param name="window" value="1" /> + <output name="output" file="output.gff" ftype="gff" /> + </test> + </tests> + <help> + +**What it does** + +Modifies the start and stop coordinates of GFF data such that the new start and stop position is based on +a specified window size that is centered on the midpoint. + + </help> + <citations> + <citation type="bibtex"> + @unpublished{None, + author = {Lai, William}, + title = {None}, + year = {None}, + eprint = {None}, + url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation} + }</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.gff Wed Jan 06 15:15:56 2016 -0500 @@ -0,0 +1,100 @@ +chr1 genetrack . 17 37 918 + . stddev=5.96715849116 +chr1 genetrack . 31 51 245 - . stddev=2.66582799529 +chr1 genetrack . 40 60 2060 + . stddev=2.7859667372 +chr1 genetrack . 62 82 1300 - . stddev=4.13061337623 +chr1 genetrack . 73 93 397 + . stddev=0.0 +chr1 genetrack . 89 109 521 + . stddev=0.747112137937 +chr1 genetrack . 123 143 5129 + . stddev=3.01025384354 +chr1 genetrack . 125 145 4659 - . stddev=3.8642622228 +chr1 genetrack . 155 175 897 - . stddev=3.22709952671 +chr1 genetrack . 171 191 956 - . stddev=4.95899971687 +chr1 genetrack . 180 200 1527 + . stddev=4.62574275346 +chr1 genetrack . 185 205 494 - . stddev=1.4255957 +chr1 genetrack . 192 212 2538 + . stddev=5.04731591122 +chr1 genetrack . 206 226 2087 - . stddev=3.6160253713 +chr1 genetrack . 238 258 2496 + . stddev=2.11105291581 +chr1 genetrack . 242 262 5047 - . stddev=3.62629343395 +chr1 genetrack . 254 274 1525 + . stddev=4.46082441647 +chr1 genetrack . 281 301 15 + . stddev=1.74610678049 +chr1 genetrack . 302 322 626 - . stddev=0.0 +chr1 genetrack . 308 328 1544 + . stddev=4.43066151722 +chr1 genetrack . 334 354 533 + . stddev=1.34355443899 +chr1 genetrack . 344 364 726 - . stddev=1.36767079956 +chr1 genetrack . 347 367 286 + . stddev=0.0 +chr1 genetrack . 358 378 792 - . stddev=1.47737416556 +chr1 genetrack . 374 394 608 + . stddev=1.44652711793 +chr1 genetrack . 389 409 126 - . stddev=0.471404520791 +chr1 genetrack . 439 459 618 - . stddev=5.47536569145 +chr1 genetrack . 441 461 1393 + . stddev=4.75587332865 +chr1 genetrack . 461 481 754 - . stddev=3.28891288785 +chr1 genetrack . 483 503 58 + . stddev=0.0 +chr1 genetrack . 538 558 1015 - . stddev=0.0 +chr1 genetrack . 728 748 39 - . stddev=0.0 +chr1 genetrack . 757 777 23 + . stddev=0.0 +chr1 genetrack . 799 819 607 + . stddev=0.0 +chr1 genetrack . 844 864 665 + . stddev=0.0 +chr1 genetrack . 877 897 468 + . stddev=0.0 +chr1 genetrack . 903 923 107 - . stddev=0.0 +chr1 genetrack . 944 964 2 - . stddev=0.0 +chr1 genetrack . 1092 1112 740 + . stddev=0.0 +chr1 genetrack . 1127 1147 940 - . stddev=3.96036497305 +chr1 genetrack . 1183 1203 25 + . stddev=0.0 +chr1 genetrack . 1291 1311 454 - . stddev=0.0 +chr1 genetrack . 1329 1349 207 - . stddev=0.0 +chr1 genetrack . 1484 1504 584 + . stddev=0.0 +chr1 genetrack . 2075 2095 1181 + . stddev=0.0 +chr1 genetrack . 2102 2122 481 + . stddev=0.0455486534308 +chr1 genetrack . 2125 2145 199 - . stddev=0.0 +chr1 genetrack . 2452 2472 1246 + . stddev=0.0 +chr1 genetrack . 2602 2622 34 + . stddev=0.0 +chr1 genetrack . 2833 2853 1062 + . stddev=1.01561431542 +chr1 genetrack . 2838 2858 1144 - . stddev=1.09438744148 +chr1 genetrack . 3011 3031 1212 - . stddev=0.0 +chr1 genetrack . 3116 3136 555 - . stddev=0.0 +chr1 genetrack . 3130 3150 17 + . stddev=0.0 +chr1 genetrack . 3378 3398 525 - . stddev=0.0 +chr1 genetrack . 3669 3689 845 + . stddev=0.0 +chr1 genetrack . 3785 3805 23 - . stddev=0.0 +chr1 genetrack . 3847 3867 316 - . stddev=0.0 +chr1 genetrack . 3868 3888 491 + . stddev=0.0 +chr1 genetrack . 4097 4117 536 - . stddev=0.0 +chr1 genetrack . 4326 4346 482 + . stddev=0.0 +chr1 genetrack . 4395 4415 3 + . stddev=0.0 +chr1 genetrack . 4461 4481 1110 + . stddev=0.0 +chr1 genetrack . 4500 4520 125 - . stddev=0.0 +chr1 genetrack . 4620 4640 147 + . stddev=0.0 +chr1 genetrack . 4826 4846 1761 + . stddev=4.82408982772 +chr1 genetrack . 4902 4922 710 + . stddev=0.0 +chr1 genetrack . 5110 5130 828 + . stddev=0.0 +chr1 genetrack . 5402 5422 282 - . stddev=0.0 +chr1 genetrack . 5501 5521 75 + . stddev=0.0 +chr1 genetrack . 5707 5727 2 + . stddev=0.0 +chr1 genetrack . 5717 5737 737 - . stddev=0.36608362591 +chr1 genetrack . 6086 6106 646 + . stddev=0.039314009595 +chr1 genetrack . 6098 6118 230 - . stddev=0.0657945476105 +chr1 genetrack . 6187 6207 329 - . stddev=0.0 +chr1 genetrack . 6290 6310 5 + . stddev=0.0 +chr1 genetrack . 6356 6376 285 + . stddev=0.0 +chr1 genetrack . 6380 6400 34 - . stddev=0.0 +chr1 genetrack . 6401 6421 1587 + . stddev=5.61831543503 +chr1 genetrack . 6415 6435 953 - . stddev=3.52372902021 +chr1 genetrack . 6432 6452 742 + . stddev=0.0 +chr1 genetrack . 6496 6516 691 + . stddev=0.0 +chr1 genetrack . 6506 6526 61 - . stddev=1.5137105198 +chr1 genetrack . 6843 6863 28 + . stddev=0.0 +chr1 genetrack . 7058 7078 518 - . stddev=0.0 +chr1 genetrack . 7124 7144 654 + . stddev=0.0 +chr1 genetrack . 7765 7785 714 + . stddev=0.0 +chr1 genetrack . 7847 7867 3 + . stddev=0.0 +chr1 genetrack . 8209 8229 17 + . stddev=0.0 +chr1 genetrack . 8272 8292 2 - . stddev=0.0 +chr1 genetrack . 8459 8479 10 + . stddev=0.0 +chr1 genetrack . 8471 8491 5 - . stddev=0.0 +chr1 genetrack . 8715 8735 5 + . stddev=0.0 +chr1 genetrack . 8834 8854 332 + . stddev=0.0 +chr1 genetrack . 8839 8859 593 - . stddev=0.0 +chr1 genetrack . 9034 9054 24 + . stddev=0.0 +chr1 genetrack . 9058 9078 4 + . stddev=0.0 +chr1 genetrack . 9485 9505 36 + . stddev=0.0 +chr1 genetrack . 9710 9730 480 + . stddev=0.0 +chr1 genetrack . 9923 9943 606 - . stddev=0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.gff Wed Jan 06 15:15:56 2016 -0500 @@ -0,0 +1,100 @@ +chr1 genetrack . 26.5 26.5 918 + . stddev=5.96715849116 +chr1 genetrack . 41.5 41.5 245 - . stddev=2.66582799529 +chr1 genetrack . 49.5 49.5 2060 + . stddev=2.7859667372 +chr1 genetrack . 72.5 72.5 1300 - . stddev=4.13061337623 +chr1 genetrack . 82.5 82.5 397 + . stddev=0.0 +chr1 genetrack . 98.5 98.5 521 + . stddev=0.747112137937 +chr1 genetrack . 132.5 132.5 5129 + . stddev=3.01025384354 +chr1 genetrack . 135.5 135.5 4659 - . stddev=3.8642622228 +chr1 genetrack . 165.5 165.5 897 - . stddev=3.22709952671 +chr1 genetrack . 181.5 181.5 956 - . stddev=4.95899971687 +chr1 genetrack . 189.5 189.5 1527 + . stddev=4.62574275346 +chr1 genetrack . 195.5 195.5 494 - . stddev=1.4255957 +chr1 genetrack . 201.5 201.5 2538 + . stddev=5.04731591122 +chr1 genetrack . 216.5 216.5 2087 - . stddev=3.6160253713 +chr1 genetrack . 247.5 247.5 2496 + . stddev=2.11105291581 +chr1 genetrack . 252.5 252.5 5047 - . stddev=3.62629343395 +chr1 genetrack . 263.5 263.5 1525 + . stddev=4.46082441647 +chr1 genetrack . 290.5 290.5 15 + . stddev=1.74610678049 +chr1 genetrack . 312.5 312.5 626 - . stddev=0.0 +chr1 genetrack . 317.5 317.5 1544 + . stddev=4.43066151722 +chr1 genetrack . 343.5 343.5 533 + . stddev=1.34355443899 +chr1 genetrack . 354.5 354.5 726 - . stddev=1.36767079956 +chr1 genetrack . 356.5 356.5 286 + . stddev=0.0 +chr1 genetrack . 368.5 368.5 792 - . stddev=1.47737416556 +chr1 genetrack . 383.5 383.5 608 + . stddev=1.44652711793 +chr1 genetrack . 399.5 399.5 126 - . stddev=0.471404520791 +chr1 genetrack . 449.5 449.5 618 - . stddev=5.47536569145 +chr1 genetrack . 450.5 450.5 1393 + . stddev=4.75587332865 +chr1 genetrack . 471.5 471.5 754 - . stddev=3.28891288785 +chr1 genetrack . 492.5 492.5 58 + . stddev=0.0 +chr1 genetrack . 548.5 548.5 1015 - . stddev=0.0 +chr1 genetrack . 738.5 738.5 39 - . stddev=0.0 +chr1 genetrack . 766.5 766.5 23 + . stddev=0.0 +chr1 genetrack . 808.5 808.5 607 + . stddev=0.0 +chr1 genetrack . 853.5 853.5 665 + . stddev=0.0 +chr1 genetrack . 886.5 886.5 468 + . stddev=0.0 +chr1 genetrack . 913.5 913.5 107 - . stddev=0.0 +chr1 genetrack . 954.5 954.5 2 - . stddev=0.0 +chr1 genetrack . 1101.5 1101.5 740 + . stddev=0.0 +chr1 genetrack . 1137.5 1137.5 940 - . stddev=3.96036497305 +chr1 genetrack . 1192.5 1192.5 25 + . stddev=0.0 +chr1 genetrack . 1301.5 1301.5 454 - . stddev=0.0 +chr1 genetrack . 1339.5 1339.5 207 - . stddev=0.0 +chr1 genetrack . 1493.5 1493.5 584 + . stddev=0.0 +chr1 genetrack . 2084.5 2084.5 1181 + . stddev=0.0 +chr1 genetrack . 2111.5 2111.5 481 + . stddev=0.0455486534308 +chr1 genetrack . 2135.5 2135.5 199 - . stddev=0.0 +chr1 genetrack . 2461.5 2461.5 1246 + . stddev=0.0 +chr1 genetrack . 2611.5 2611.5 34 + . stddev=0.0 +chr1 genetrack . 2842.5 2842.5 1062 + . stddev=1.01561431542 +chr1 genetrack . 2848.5 2848.5 1144 - . stddev=1.09438744148 +chr1 genetrack . 3021.5 3021.5 1212 - . stddev=0.0 +chr1 genetrack . 3126.5 3126.5 555 - . stddev=0.0 +chr1 genetrack . 3139.5 3139.5 17 + . stddev=0.0 +chr1 genetrack . 3388.5 3388.5 525 - . stddev=0.0 +chr1 genetrack . 3678.5 3678.5 845 + . stddev=0.0 +chr1 genetrack . 3795.5 3795.5 23 - . stddev=0.0 +chr1 genetrack . 3857.5 3857.5 316 - . stddev=0.0 +chr1 genetrack . 3877.5 3877.5 491 + . stddev=0.0 +chr1 genetrack . 4107.5 4107.5 536 - . stddev=0.0 +chr1 genetrack . 4335.5 4335.5 482 + . stddev=0.0 +chr1 genetrack . 4404.5 4404.5 3 + . stddev=0.0 +chr1 genetrack . 4470.5 4470.5 1110 + . stddev=0.0 +chr1 genetrack . 4510.5 4510.5 125 - . stddev=0.0 +chr1 genetrack . 4629.5 4629.5 147 + . stddev=0.0 +chr1 genetrack . 4835.5 4835.5 1761 + . stddev=4.82408982772 +chr1 genetrack . 4911.5 4911.5 710 + . stddev=0.0 +chr1 genetrack . 5119.5 5119.5 828 + . stddev=0.0 +chr1 genetrack . 5412.5 5412.5 282 - . stddev=0.0 +chr1 genetrack . 5510.5 5510.5 75 + . stddev=0.0 +chr1 genetrack . 5716.5 5716.5 2 + . stddev=0.0 +chr1 genetrack . 5727.5 5727.5 737 - . stddev=0.36608362591 +chr1 genetrack . 6095.5 6095.5 646 + . stddev=0.039314009595 +chr1 genetrack . 6108.5 6108.5 230 - . stddev=0.0657945476105 +chr1 genetrack . 6197.5 6197.5 329 - . stddev=0.0 +chr1 genetrack . 6299.5 6299.5 5 + . stddev=0.0 +chr1 genetrack . 6365.5 6365.5 285 + . stddev=0.0 +chr1 genetrack . 6390.5 6390.5 34 - . stddev=0.0 +chr1 genetrack . 6410.5 6410.5 1587 + . stddev=5.61831543503 +chr1 genetrack . 6425.5 6425.5 953 - . stddev=3.52372902021 +chr1 genetrack . 6441.5 6441.5 742 + . stddev=0.0 +chr1 genetrack . 6505.5 6505.5 691 + . stddev=0.0 +chr1 genetrack . 6516.5 6516.5 61 - . stddev=1.5137105198 +chr1 genetrack . 6852.5 6852.5 28 + . stddev=0.0 +chr1 genetrack . 7068.5 7068.5 518 - . stddev=0.0 +chr1 genetrack . 7133.5 7133.5 654 + . stddev=0.0 +chr1 genetrack . 7774.5 7774.5 714 + . stddev=0.0 +chr1 genetrack . 7856.5 7856.5 3 + . stddev=0.0 +chr1 genetrack . 8218.5 8218.5 17 + . stddev=0.0 +chr1 genetrack . 8282.5 8282.5 2 - . stddev=0.0 +chr1 genetrack . 8468.5 8468.5 10 + . stddev=0.0 +chr1 genetrack . 8481.5 8481.5 5 - . stddev=0.0 +chr1 genetrack . 8724.5 8724.5 5 + . stddev=0.0 +chr1 genetrack . 8843.5 8843.5 332 + . stddev=0.0 +chr1 genetrack . 8849.5 8849.5 593 - . stddev=0.0 +chr1 genetrack . 9043.5 9043.5 24 + . stddev=0.0 +chr1 genetrack . 9067.5 9067.5 4 + . stddev=0.0 +chr1 genetrack . 9494.5 9494.5 36 + . stddev=0.0 +chr1 genetrack . 9719.5 9719.5 480 + . stddev=0.0 +chr1 genetrack . 9933.5 9933.5 606 - . stddev=0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Jan 06 15:15:56 2016 -0500 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="perl" version="5.18.1"> + <repository changeset_revision="6f144bd786a8" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>