details: http://www.bx.psu.edu/hg/galaxy/rev/d53da5b089a8 changeset: 1662:d53da5b089a8 user: guru date: Fri Dec 12 12:12:59 2008 -0500 description: Added more test-cases to GOPS JOIN to include cases with different cut-offs for overlap. 3 file(s) affected in this change: test-data/gops-join-both-100.dat test-data/gops-join-none-500.dat tools/new_operations/join.xml diffs (139 lines): diff -r 8e3d63d7cd8a -r d53da5b089a8 test-data/gops-join-both-100.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops-join-both-100.dat Fri Dec 12 12:12:59 2008 -0500 @@ -0,0 +1,99 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - chr1 147962192 147962580 NM_005997_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + . . . . . . +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - . . . . . . +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + . . . . . . +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + . . . . . . +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - . . . . . . +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + . . . . . . +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + . . . . . . +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - . . . . . . +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + . . . . . . +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + . . . . . . +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - . . . . . . +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + . . . . . . +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - . . . . . . +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + . . . . . . +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - . . . . . . +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - . . . . . . +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + . . . . . . +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + . . . . . . +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - . . . . . . +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + . . . . . . +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + . . . . . . +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - . . . . . . +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - . . . . . . +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + . . . . . . +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - . . . . . . +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + . . . . . . +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + . . . . . . +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + . . . . . . +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + . . . . . . +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - . . . . . . +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + . . . . . . +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 - +. . . . . . chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 + +. . . . . . chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 + +. . . . . . chr5 131311206 131311254 AF099740_cds_11_0_chr5_131311207_r 0 - +. . . . . . chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 - +. . . . . . chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 + +. . . . . . chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 + +. . . . . . chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 + +. . . . . . chr2 118390395 118390500 BC005078_cds_0_0_chr2_118390396_r 0 - +. . . . . . chr2 220108689 220109267 AY125465_cds_0_0_chr2_220108690_f 0 + +. . . . . . chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 + +. . . . . . chr21 32687402 32687588 NM_032910_cds_0_0_chr21_32687403_f 0 + +. . . . . . chr21 33728358 33728724 AK129657_cds_0_0_chr21_33728359_r 0 - +. . . . . . chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 + +. . . . . . chr9 128789552 128789584 NM_015354_cds_0_0_chr9_128789553_f 0 + +. . . . . . chr9 128850516 128850624 AB058751_cds_0_0_chr9_128850517_r 0 - +. . . . . . chr13 29680676 29680875 NM_032116_cds_0_0_chr13_29680677_r 0 - +. . . . . . chr12 38905200 38905351 AY792511_cds_0_0_chr12_38905201_f 0 + +. . . . . . chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 - +. . . . . . chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 + +. . . . . . chr11 130745911 130745993 AY358331_cds_0_0_chr11_130745912_f 0 + +. . . . . . chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 + +. . . . . . chr22 30228824 30228916 NM_001007467_cds_1_0_chr22_30228825_f 0 + +. . . . . . chr22 30340151 30340376 CR456540_cds_0_0_chr22_30340152_r 0 - +. . . . . . chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 + +. . . . . . chr16 179197 179339 BC065198_cds_0_0_chr16_179198_r 0 - +. . . . . . chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 - +. . . . . . chr15 41773540 41773689 AK223365_cds_0_0_chr15_41773541_f 0 + +. . . . . . chr14 98521864 98521922 U88895_cds_0_0_chr14_98521865_f 0 + +. . . . . . chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 - +. . . . . . chr20 33485370 33486123 BC085019_cds_1_0_chr20_33485371_f 0 + +. . . . . . chr20 33488491 33489122 NM_000557_cds_1_0_chr20_33488492_r 0 - +. . . . . . chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 + +. . . . . . chr19 59318205 59318718 AK128544_cds_3_0_chr19_59318206_r 0 - +. . . . . . chr18 59528407 59528575 AY792326_cds_0_0_chr18_59528408_f 0 + diff -r 8e3d63d7cd8a -r d53da5b089a8 test-data/gops-join-none-500.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops-join-none-500.dat Fri Dec 12 12:12:59 2008 -0500 @@ -0,0 +1,8 @@ +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 - +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 - +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 - +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 + diff -r 8e3d63d7cd8a -r d53da5b089a8 tools/new_operations/join.xml --- a/tools/new_operations/join.xml Fri Dec 12 11:53:06 2008 -0500 +++ b/tools/new_operations/join.xml Fri Dec 12 12:12:59 2008 -0500 @@ -51,6 +51,20 @@ <param name="fill" value="both" /> <output name="output" file="gops-join-both.dat" /> </test> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2.bed" /> + <param name="min" value="500" /> + <param name="fill" value="none" /> + <output name="output" file="gops-join-none-500.dat" /> + </test> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2.bed" /> + <param name="min" value="100" /> + <param name="fill" value="both" /> + <output name="output" file="gops-join-both-100.dat" /> + </test> </tests> <help>