Mercurial > repos > devteam > windowsplitter
changeset 0:e5490ea33640
Imported from capsule None
| author | devteam |
|---|---|
| date | Tue, 01 Apr 2014 10:50:03 -0400 |
| parents | |
| children | 75abda2290cc |
| files | test-data/4.bed test-data/4_windows.bed windowSplitter.py windowSplitter.xml |
| diffstat | 4 files changed, 613 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4.bed Tue Apr 01 10:50:03 2014 -0400 @@ -0,0 +1,1 @@ +chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4_windows.bed Tue Apr 01 10:50:03 2014 -0400 @@ -0,0 +1,424 @@ +chr22 30128507 30133507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30132507 30137507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30136507 30141507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30140507 30145507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30144507 30149507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30148507 30153507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30152507 30157507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30156507 30161507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30160507 30165507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30164507 30169507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30168507 30173507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30172507 30177507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30176507 30181507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30180507 30185507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30184507 30189507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30188507 30193507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30192507 30197507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30196507 30201507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30200507 30205507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30204507 30209507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30208507 30213507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30212507 30217507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30216507 30221507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30220507 30225507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30224507 30229507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30228507 30233507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30232507 30237507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30236507 30241507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30240507 30245507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30244507 30249507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30248507 30253507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30252507 30257507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30256507 30261507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30260507 30265507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30264507 30269507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30268507 30273507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30272507 30277507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30276507 30281507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30280507 30285507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30284507 30289507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30288507 30293507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30292507 30297507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30296507 30301507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30300507 30305507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30304507 30309507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30308507 30313507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30312507 30317507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30316507 30321507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30320507 30325507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30324507 30329507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30328507 30333507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30332507 30337507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30336507 30341507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30340507 30345507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30344507 30349507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30348507 30353507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30352507 30357507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30356507 30361507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30360507 30365507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30364507 30369507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30368507 30373507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30372507 30377507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30376507 30381507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30380507 30385507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30384507 30389507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30388507 30393507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30392507 30397507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30396507 30401507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30400507 30405507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30404507 30409507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30408507 30413507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30412507 30417507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30416507 30421507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30420507 30425507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30424507 30429507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30428507 30433507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30432507 30437507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30436507 30441507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30440507 30445507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30444507 30449507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30448507 30453507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30452507 30457507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30456507 30461507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30460507 30465507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30464507 30469507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30468507 30473507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30472507 30477507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30476507 30481507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30480507 30485507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30484507 30489507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30488507 30493507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30492507 30497507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30496507 30501507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30500507 30505507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30504507 30509507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30508507 30513507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30512507 30517507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30516507 30521507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30520507 30525507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30524507 30529507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30528507 30533507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30532507 30537507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30536507 30541507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30540507 30545507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30544507 30549507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30548507 30553507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30552507 30557507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30556507 30561507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30560507 30565507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30564507 30569507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30568507 30573507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30572507 30577507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30576507 30581507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30580507 30585507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30584507 30589507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30588507 30593507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30592507 30597507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30596507 30601507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30600507 30605507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30604507 30609507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30608507 30613507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30612507 30617507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30616507 30621507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30620507 30625507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30624507 30629507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30628507 30633507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30632507 30637507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30636507 30641507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30640507 30645507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30644507 30649507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30648507 30653507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30652507 30657507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30656507 30661507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30660507 30665507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30664507 30669507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30668507 30673507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30672507 30677507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30676507 30681507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30680507 30685507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30684507 30689507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30688507 30693507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30692507 30697507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30696507 30701507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30700507 30705507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30704507 30709507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30708507 30713507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30712507 30717507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30716507 30721507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30720507 30725507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30724507 30729507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30728507 30733507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30732507 30737507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30736507 30741507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30740507 30745507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30744507 30749507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30748507 30753507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30752507 30757507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30756507 30761507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30760507 30765507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30764507 30769507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30768507 30773507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30772507 30777507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30776507 30781507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30780507 30785507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30784507 30789507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30788507 30793507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30792507 30797507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30796507 30801507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30800507 30805507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30804507 30809507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30808507 30813507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30812507 30817507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30816507 30821507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30820507 30825507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30824507 30829507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30828507 30833507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30832507 30837507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30836507 30841507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30840507 30845507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30844507 30849507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30848507 30853507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30852507 30857507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30856507 30861507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30860507 30865507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30864507 30869507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30868507 30873507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30872507 30877507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30876507 30881507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30880507 30885507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30884507 30889507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30888507 30893507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30892507 30897507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30896507 30901507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30900507 30905507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30904507 30909507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30908507 30913507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30912507 30917507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30916507 30921507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30920507 30925507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30924507 30929507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30928507 30933507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30932507 30937507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30936507 30941507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30940507 30945507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30944507 30949507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30948507 30953507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30952507 30957507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30956507 30961507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30960507 30965507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30964507 30969507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30968507 30973507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30972507 30977507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30976507 30981507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30980507 30985507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30984507 30989507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30988507 30993507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30992507 30997507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 30996507 31001507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31000507 31005507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31004507 31009507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31008507 31013507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31012507 31017507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31016507 31021507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31020507 31025507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31024507 31029507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31028507 31033507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31032507 31037507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31036507 31041507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31040507 31045507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31044507 31049507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31048507 31053507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31052507 31057507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31056507 31061507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31060507 31065507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31064507 31069507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31068507 31073507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31072507 31077507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31076507 31081507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31080507 31085507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31084507 31089507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31088507 31093507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31092507 31097507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31096507 31101507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31100507 31105507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31104507 31109507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31108507 31113507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31112507 31117507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31116507 31121507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31120507 31125507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31124507 31129507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31128507 31133507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31132507 31137507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31136507 31141507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31140507 31145507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31144507 31149507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31148507 31153507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31152507 31157507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31156507 31161507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31160507 31165507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31164507 31169507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31168507 31173507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31172507 31177507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31176507 31181507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31180507 31185507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31184507 31189507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31188507 31193507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31192507 31197507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31196507 31201507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31200507 31205507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31204507 31209507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31208507 31213507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31212507 31217507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31216507 31221507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31220507 31225507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31224507 31229507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31228507 31233507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31232507 31237507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31236507 31241507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31240507 31245507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31244507 31249507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31248507 31253507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31252507 31257507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31256507 31261507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31260507 31265507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31264507 31269507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31268507 31273507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31272507 31277507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31276507 31281507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31280507 31285507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31284507 31289507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31288507 31293507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31292507 31297507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31296507 31301507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31300507 31305507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31304507 31309507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31308507 31313507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31312507 31317507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31316507 31321507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31320507 31325507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31324507 31329507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31328507 31333507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31332507 31337507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31336507 31341507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31340507 31345507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31344507 31349507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31348507 31353507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31352507 31357507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31356507 31361507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31360507 31365507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31364507 31369507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31368507 31373507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31372507 31377507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31376507 31381507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31380507 31385507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31384507 31389507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31388507 31393507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31392507 31397507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31396507 31401507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31400507 31405507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31404507 31409507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31408507 31413507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31412507 31417507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31416507 31421507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31420507 31425507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31424507 31429507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31428507 31433507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31432507 31437507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31436507 31441507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31440507 31445507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31444507 31449507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31448507 31453507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31452507 31457507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31456507 31461507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31460507 31465507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31464507 31469507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31468507 31473507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31472507 31477507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31476507 31481507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31480507 31485507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31484507 31489507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31488507 31493507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31492507 31497507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31496507 31501507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31500507 31505507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31504507 31509507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31508507 31513507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31512507 31517507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31516507 31521507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31520507 31525507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31524507 31529507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31528507 31533507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31532507 31537507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31536507 31541507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31540507 31545507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31544507 31549507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31548507 31553507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31552507 31557507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31556507 31561507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31560507 31565507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31564507 31569507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31568507 31573507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31572507 31577507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31576507 31581507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31580507 31585507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31584507 31589507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31588507 31593507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31592507 31597507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31596507 31601507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31600507 31605507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31604507 31609507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31608507 31613507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31612507 31617507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31616507 31621507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31620507 31625507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31624507 31629507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31628507 31633507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31632507 31637507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31636507 31641507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31640507 31645507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31644507 31649507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31648507 31653507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31652507 31657507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31656507 31661507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31660507 31665507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31664507 31669507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31668507 31673507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31672507 31677507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31676507 31681507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31680507 31685507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31684507 31689507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31688507 31693507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31692507 31697507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31696507 31701507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31700507 31705507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31704507 31709507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31708507 31713507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31712507 31717507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31716507 31721507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31720507 31725507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31724507 31729507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31728507 31733507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31732507 31737507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31736507 31741507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31740507 31745507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31744507 31749507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31748507 31753507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31752507 31757507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31756507 31761507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31760507 31765507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31764507 31769507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31768507 31773507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31772507 31777507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31776507 31781507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31780507 31785507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31784507 31789507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31788507 31793507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31792507 31797507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31796507 31801507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31800507 31805507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31804507 31809507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31808507 31813507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31812507 31817507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31816507 31821507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + +chr22 31820507 31825507 uc003bnx.1_cds_2_0_chr22_29227_f 0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/windowSplitter.py Tue Apr 01 10:50:03 2014 -0400 @@ -0,0 +1,84 @@ +#!/usr/bin/env python + +""" +Split into windows. + +usage: %prog input size out_file + -l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file +""" + +import sys + +from galaxy import eggs +import pkg_resources +pkg_resources.require( "bx-python" ) +from bx.cookbook import doc_optparse +from galaxy.tools.util.galaxyops import * + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + + +def main(): + # Parsing Command Line here + options, args = doc_optparse.parse( __doc__ ) + + try: + chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols ) + inp_file, winsize, out_file, makesliding, offset = args + winsize = int(winsize) + offset = int(offset) + makesliding = int(makesliding) + except: + stop_err( "Data issue, click the pencil icon in the history item to correct the metadata attributes of the input dataset." ) + + fo = open(out_file,'w') + + skipped_lines = 0 + first_invalid_line = 0 + invalid_line = None + if offset == 0: + makesliding = 0 + + for i, line in enumerate( file( inp_file ) ): + line = line.strip() + if line and line[0:1] != "#": + try: + elems = line.split('\t') + start = int(elems[start_col_1]) + end = int(elems[end_col_1]) + if makesliding == 0: + numwin = (end - start)/winsize + else: + numwin = (end - start)/offset + if numwin > 0: + for win in range(numwin): + elems_1 = elems + elems_1[start_col_1] = str(start) + elems_1[end_col_1] = str(start + winsize) + fo.write( "%s\n" % '\t'.join( elems_1 ) ) + if makesliding == 0: + start = start + winsize + else: + start = start + offset + if start+winsize > end: + break + except: + skipped_lines += 1 + if not invalid_line: + first_invalid_line = i + 1 + invalid_line = line + + fo.close() + + if makesliding == 1: + print 'Window size=%d, Sliding=Yes, Offset=%d' % ( winsize, offset ) + else: + print 'Window size=%d, Sliding=No' % (winsize) + if skipped_lines > 0: + print 'Skipped %d invalid lines starting with #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line ) + + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/windowSplitter.xml Tue Apr 01 10:50:03 2014 -0400 @@ -0,0 +1,104 @@ +<tool id="winSplitter" name="Make windows" version="0.0.1"> + <description></description> + <command interpreter="python">windowSplitter.py $input $size $out_file1 ${wintype.choice} ${wintype.offset} -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command> + <inputs> + <!--<param label="Genome" name="dbkey" type="genomebuild"/>--> + <param format="interval" name="input" type="data" label="Select data"/> + <param name="size" size="10" type="integer" value="500" label="Window size"/> + <conditional name="wintype"> + <param name="choice" type="select" label="Make sliding windows?"> + <option value="0" selected="true">No</option> + <option value="1">Yes</option> + </param> + <when value="0"> + <param name="offset" type="hidden" value="0" /> + </when> + <when value="1"> + <param name="offset" size="10" type="integer" value="10" label="Offset size"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="interval" name="out_file1" metadata_source="input"/> + </outputs> + <tests> + <test> + <param name="input" value="4.bed"/> + <param name="size" value="5000"/> + <param name="choice" value="1"/> + <param name="offset" value="4000"/> + <output name="out_file1" file="4_windows.bed"/> + </test> + </tests> + <help> + +.. class:: infomark + +**What it does** + +This tool splits the intervals in the input file into smaller intervals based on the specified window-size and window type. + +----- + +.. class:: warningmark + +**Note** + +The positions at the end of the input interval which do not fit into the last window or a new window of required size, will be omitted from the output. + +----- + +.. class:: infomark + +**About formats** + +**BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones: + +The first three BED fields (required) are:: + + 1. chrom - The name of the chromosome (e.g. chr1, chrY_random). + 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.) + 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval). + +The additional BED fields (optional) are:: + + 4. name - The name of the BED line. + 5. score - A score between 0 and 1000. + 6. strand - Defines the strand - either '+' or '-'. + 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser. + 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser. + 9. reserved - This should always be set to zero. + 10. blockCount - The number of blocks (exons) in the BED line. + 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount. + 12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount. + 13. expCount - The number of experiments. + 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount. + 15. expScores - A comma-separated list of experiment scores. All of the expScores should be relative to expIds. The number of items in this list should correspond to expCount. + +----- + +**Example** + +- For the following dataset:: + + chr22 1000 4700 NM_174568 0 + + +- running this tool with **Window size as 1000**, will return:: + + chr22 1000 2000 NM_174568 0 + + chr22 2000 3000 NM_174568 0 + + chr22 3000 4000 NM_174568 0 + + +- running this tool to make **Sliding windows** of **size 1000** and **offset 500**, will return:: + + chr22 1000 2000 NM_174568 0 + + chr22 1500 2500 NM_174568 0 + + chr22 2000 3000 NM_174568 0 + + chr22 2500 3500 NM_174568 0 + + chr22 3000 4000 NM_174568 0 + + chr22 3500 4500 NM_174568 0 + + + </help> + + +</tool>