Mercurial > repos > greg > gene_family_phylogeny_builder
changeset 55:8013d394c525 draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 30 Oct 2017 09:05:37 -0400 |
| parents | eef0f4704dca |
| children | 178971bba68f |
| files | plant_tribes_scaffolds.loc test-data/3722.faa.aln test-data/3722.faa.aln.tree test-data/tool-data/plant_tribes/scaffolds/README.txt tool_data_table_conf.xml.test utils.py |
| diffstat | 6 files changed, 325 insertions(+), 26 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plant_tribes_scaffolds.loc Mon Oct 30 09:05:37 2017 -0400 @@ -0,0 +1,3 @@ +## Plant Tribes scaffolds +#Value Name Path Description +22Gv1.1 22Gv1.1 ${__HERE__}/test-data/tool-data/plant_tribes/scaffolds/22Gv1.1 22 plant genomes (Angiosperms clusters, version 1.1; 22Gv1.1)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3722.faa.aln Mon Oct 30 09:05:37 2017 -0400 @@ -0,0 +1,312 @@ +>gnl_Glyma1.01_PACid_16266208 +---MANE-------------------------------------------------GKKS +NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY +S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG +--EESFEELQ------QLFEDMFQADI--GL----------DGGPSL------------- +----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM +NFGK---AENSSVFDASY------QNFCFG-VN--QLQDIKKGK---GGILGGGGRSRHR +SGRKQKMFY-GHDV-------------------------- +>gnl_Glyma1.01_PACid_16266209 +---MANE-------------------------------------------------GKKS +NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY +S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG +--EESFEELQ------QLFEDMFQADI--GL----------DGGPSL------------- +----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM +NFGK---AENSSVFDASY------QNFCFG-TG--EPTPRYKEG--------KGGNSRRR +R--------------------------------------- +>gnl_Glyma1.01_PACid_16266210 +---MANE-------------------------------------------------GKKS +NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY +S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG +--EESFEELQ------QLFEDMFQADI--GL----------DGGPSL------------- +----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM +NFGK---AENSSVFDASY------QNFCFG-VG--HVNYHYQ------------------ +---------------------------------------- +>gnl_Glyma1.01_PACid_16301083 +---MADE-------------------------------------------------GNKS +NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY +S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG +--EESFEELQ------QLFEDMFEADI--GL----------DGGPSL------------- +----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM +NFGK---AENSSVFDAGY------QNFCFG-VN--QLQDIKKKK---GGIL-GGGRSRHR +NGRKQNMSY-GHDVSSNDYPGISTK--------------- +>gnl_Glyma1.01_PACid_16301085 +---MADE-------------------------------------------------GNKS +NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY +S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG +--EESFEELQ------QLFEDMFEADI--GL----------DGGPSL------------- +----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM +NFGK---AENSSVFDAGY------QNFCFG-VG--HVNYHYQ------------------ +---------------------------------------- +>gnl_Glyma1.01_PACid_16301084 +---MADE-------------------------------------------------GNKS +NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY +S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG +--EESFEELQ------QLFEDMFEADI--GL----------DGGPSL------------- +----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM +NFGK---AENSSVFDAGY------QNFCFG-TG--EPTPRYKEE--------KGGNSRRR +---------------------------------------- +>gnl_Medtr3.5_Medtr8g022310.1 +---MANE-------------------------------------------------GNKS +NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY +S------VLSDSNKRLMYDVGVYDS--------DDDENGMGDFLNEMVTMMSQTKSNENG +--EESFEELQ------QLFDDMFQADI--GL----------NGSTSL------------- +----NASGCSTSST------------------FMTFSESSN---------SNKRNST-QM +NFGK---AEDSSSFGANY------QNFCFG-MK--HLQEDVEKE--KGGILEGGGSKKQR +KGRKQKISC-GH-VSSNDHPGISAN--------------- +>gnl_Medtr3.5_Medtr8g022310.2 +---MANE-------------------------------------------------GNKS +NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY +S------VLSDSNKRLMYDVGVYDS--------DDDENGMGDFLNEMVTMMSQTKSNENG +--EESFEELQ------QLFDDMFQADI--GL----------NGSTSL------------- +----NASGCSTSST------------------FMTFSESSN---------SNKRNST-QM +NFGK---AEDSSSFGANY------QNFCFG-VN--LVNYHYQ------------------ +---------------------------------------- +>gnl_Musac1.0_GSMUA_Achr6T31040_001 +---MAAE-------------------------------------------------EDKS +GDFYAVLGLRKECSETELRNAYKKLAMRWHPDKCLASG---NAQIVGEAKEKFQEIQKAY +S------VLSDSNKRFLYDVGVYDND------DDNDENGMGDFIGEMLEMMSQTKPNENS +--QDSFQELQ------ELFVEMFQDDL--DAG---------FGGSIFH-DCPWAQP---- +---TNGQDCWTSSG------------------LHFANGRSK--------CGNKRGNS-AV +NLGK----VNLEELEHGT------SDFYFG-LN--DAAQPSQGKGGS--------NNKRR +NGRKQKVSS-NHDVSS------------------------ +>gnl_Musac1.0_GSMUA_Achr9T18140_001 +---MAAG-------------------------------------------------EEKI +GDFYTVLGLRKECSEAELRIAYKKLAMRWHPDKCSASG---NHRRMEEAKEKFQEIQKAY +S------VLSDSSKRFLYDVGIYDNE------DDNDEKGMGDFIGEIAQMMSQTKSGENG +--HDSFEELQ------RMFLDMFQDDL--DAG---------FGDSSIH-SGPQARP---- +---TDGLNCSMPSG------------------LQFADGGNN--------GSNKRGNS-EK +--------AKLDGLENSS------TGFCFG-LN--DAGQSSKGKGSA--------NSKRR +NGRKQKVSS-KHDVSSSD-AEVSF---------------- +>gnl_Musac1.0_GSMUA_Achr8T23700_001 +---MASD-------------------------------------------------MDAS +GDFYSVLGLKKECSEAELRNAYKKLALKWHPDKCSASG---NEIRMKEAKQQFQEIQKAY +S------VLSDSNKRFLYDVGAYDKD------DDKDEEGMVEFLGEMAQMMRQTKCCGSG +--QESFEQLQ------QMFVEMFHDDL--DAG---------F------------------ +--------CGHSSA---------------------TSGAAS--------CGNKRDNS-AM +DSGK----RKPDELDPAA------IGFCLG-TK--DAGQSSKGRGS---------NSKRR +NRRKQKASS-KHDNSSHN-AKVSA---------------- +>gnl_Musac1.0_GSMUA_AchrUn_randomT02210_001 +---MEGD-------------------------------------------------EEKS +GDFYAVLGLKKEGSMAELKNAYKKLAMKWHPDKCPASG---NKIRMDKAKEKFQEIQKAY +S------VLSDSNKRFLYDVGVYDKD------DEEDEEGMGDFIGEIAQMMSQSKPSGSG +--HESLEELH------RQVVEMFLDEL--DAGD-------RFSSANQ------------- +----GASSCDGRDD----------------------------------GGGNKRGNW-AV +DWGK----EKLNELGPGT------GGFCFG-VS------------------------RRV +HSFDLMIDV-VHLIHSDL-------------------TLE +>gnl_Orysa6.0_PACid_16843526 +---MADGG-------------------------------------EKC-RDAAG-EGGGG +GDLYAVLGLKKECSDADLKLAYRKLAMRWHPDKCSSSS---SAKHMEEAKEKFQEIQGAY +S------VLSDSNKRFLYDVGVYDDDD----NDDDNLQGMGDFIGEMAQMMSQARPTR-- +--QESFKELQ------QLFVDMFQADL--DSG---------FCNGPSKCYHTQAQSQTRT +SSTSPSMSPSPPPP------------------VATEAESPS------CNGINKRGSS-AM +DSGK-PPRASEVGSGQSQ------SGFCFG-KS--DAKQAAKTRSGNT-------ASRRR +NGRKQKVSS-KHDVSSEDEMPGSQW-----------HGVA +>gnl_Orysa6.0_PACid_16843528 +---MADGG-------------------------------------EKC-RDAAG-EGGGG +GDLYAVLGLKKECSDADLKLAYRKLAMRWHPDKCSSSS---SAKHMEEAKEKFQEIQGAY +S------VLSDSNKRFLYDVGVYDDDD----NDDDNLQGMGDFIGEMAQMMSQARPTR-- +--QESFKELQ------QLFVDMFQADL--DSG---------FCNGPSKCYHTQAQSQTRT +SSTSPSMSPSPPPP------------------VATEAESPS------CNGINKRGSS-AM +DSGK-PPRASEVGSGQSQ------SGFCFGQKS--DAKQAAKTRSGNT-------ASRRR +NGRKQKVSS-KHDVSSEDEMPGSQW-----------HGVA +>gnl_Poptr2.2_PACid_18217800 +---MANGGE----------------------------------------------DKWKS +NDLYQVLGLNKECTDTELRSAYKKLALRWHPDRCSASG---NSKFVEEAKKKFQAIQQAY +S------VLSDTNKRFLYDVGVDDS--------DDDENGMGDFLNEMAVMMSQTKPSENM +--EESLEELQ------ELFDEMFQEDL--HS----------FGIDSQ------------- +----AAPSC--PPS------------------YVSYSESSN--------SNNKRVSA-DM +NLGK-TKVDDSSSFNSHF------EKFCLG-T-----------GGTAATFQEGEGGSKRR +NSRRSQRQT-KARQETKSFFGL------------------ +>gnl_Poptr2.2_PACid_18234651 +---MENGGE----------------------------------------------EKGKS +NDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASE---NSRFVDEAKKKFQTIQQAY +S------VLSDTNKRFLYDVGVYDS--------EDDENGMGGFMNEMAAMMSQTKPHENV +--EESFEELQ------GLFEEMFQEDL--DS----------FGIACQ------------- +----ATT-------------------------CVSYSESSN--------SNDKRVSV-DM +NLKK-TKVDDSSGFNSHV------EKFCLG-V-----------SGTPAIFQEGE-GSKRR +SSRRNRR--------------------------------- +>gnl_Poptr2.2_PACid_18234649 +MLRMENGGE----------------------------------------------EKGKS +NDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASE---NSRFVDEAKKKFQTIQQAY +S------VLSDTNKRFLYDVGVYDS--------EDDENGMGGFMNEMAAMMSQTKPHENV +--EESFEELQ------GLFEEMFQEDL--DS----------FGIACQ------------- +----ATT-------------------------CVSYSESSN--------SNDKRVSV-DM +NLKK-TKVDDSSGFNSHV------EKFCLG-VE--HQQSFKKGKGVRGGVQGGT-GGRER +KGRKQEVSS-GYDVSSHD-HGISAS--------------- +>gnl_Poptr2.2_PACid_18234650 +---MENGGE----------------------------------------------EKGKS +NDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASE---NSRFVDEAKKKFQTIQQAY +S------VLSDTNKRFLYDVGVYDS--------EDDENGMGGFMNEMAAMMSQTKPHENV +--EESFEELQ------GLFEEMFQEDL--DS----------FGIACQ------------- +----ATT-------------------------CVSYSESSN--------SNDKRVSV-DM +NLKK-TKVDDSSGFNSHV------EKFCLG-VE--HQQSFKKGKGVRGGVQGGT-GGRER +KGRKQEVSS-GYDVSSHD-HGISAS--------------- +>gnl_Soltu3.4_PGSC0003DMP400016105 +---M-------------------------------------------------------G +NDYYAVLGLKKECTETELRNAYKKLALKWHPDRCSASG---NSKFVDEAKKKFQAIQEAY +S------VLSDANKRFLYDVGVYDSG------DDDDENGMGDFLNEMAAMMSQNKSNENQ +--EETFEELQ------DMFDEIFNSDN--GM------------SSSS------------- +----SSSSRTGTPS------------------MCSTTSSTSSSET-FFTFSNKRSSG-EM +KSGK--------GDSCQF------QGFCEG-T-----------GGASGKSNERE-RSRRK +NSKSGRKQ-------------------------------- +>gnl_Soltu3.4_PGSC0003DMP400016106 +---M-------------------------------------------------------G +NDYYAVLGLKKECTETELRNAYKKLALKWHPDRCSASG---NSKFVDEAKKKFQAIQEAY +S------VLSDANKRFLYDVGVYDSG------DDDDENGMGDFLNEMAAMMSQNKSNENQ +--EETFEELQ------DMFDEIFNSDN--GM------------SSSS------------- +----SSSSRTGTPS------------------MCSTTSSTSSSET-FFTFSNKRSSG-EM +KSGK--------GDSCQF------QGFCEG-VE--HLEKAMKENGVGGKIPRVD-GSNRM +DAKRQKVLS------------------------------- +>gnl_Ambtr1.0.27_AmTr_v1.0_scaffold00007.329 +---MAPR-------------------------------------------------GEKD +SDFYAILGLKKECSASDLRNAYKRLALRWHPDRCSASG---NTKFVEECKKKFQAIQQAY +S------VLSDANKRFLYDVGAYGS--------DDDDQGMGEFLGEMAVMMSQTKPSEKG +--PESFEDLQ------NLFQEMFERDL--DM----------FKSSTSH------------ +----NNNNDNNNNN------------------HRSSDNNNCSSVH-CFSNTNKRNCS-DM +NAGE-ASEVGRFAFSCYATEFLHKQTFSVG-AD------DVRSES----------SNKRR +NGRKQKSTS-SSRKS------------------------- +>gnl_Aquco1.0_PACid_18141277 +---MAS--------------------------------------------------EEEA +SDFYKVLGLKNNCSSLELRNAYKKLALKWHPDRCAASG---NSKFVEEAKKNFQAIQEAY +S------VLSDEQKRFMYDVGVYDKD------DDDENEDMGDFLGEMMSMMKQENTSADG +--QQSFEDLQ------NLFQEMVQNDK--EF----------YNPASQ------------- +----NSSIYNASNNMFSFSNNENLNNASNNTFSSFYNENLN--------SSNKKSCS-SM +SAEN--TKVDFNMESLDF------RSFSIG-LE--GGTSFQNSKGRG--------VTGRR +TGRKQKGSS-CNDMSSHD-SKILA---------------- +>gnl_Arath10_AT3G14200.1 +---MASSN-----------------------------------------------SEKIN +ENLYAVLGLKKECSKTELRSAYKKLALRWHPDRCSS------MEFVEEAKKKFQAIQEAY +S------VLSDSNKRFLYDVGAYNTD------DDDDQNGMGDFLNEMATMMNQSKPSDNN +-TGDSFEQLQ------DLFNEMFQGDA--AA----------FPSS--------------- +------SSCSTSNF------------------TSSRSFVFD--------TNSQRSSSFAT +SSMG--MNNDPFGYDPRA------HSFSLG-VD--HQQEFKKGKN----------NGGRR +NRRKNNVPSAGHETSSSNNYGVPTS--------------- +>gnl_Bradi1.2_Bradi3g60090.1 +---MATGG-------------------------------------DKCGGKPAA-AGVGG +GDLYSVLGVNKECSDADLKVAYRKLAMRWHPDRCSSSS---STKHMEEAKEKFQEIQGAY +S------VLSDANKRFLYDVGVYEEHEE---EDDDTLQGMGDFLGEMAHMMSQTQPAR-- +--QESFEELQ------QLFVDMFQSDI--ESG---------FCNGPAK-DHDPVQRQTRT +FSTPPSPSPSPPPP------------------LATVDEAAS------CNGINKRGSS-AM +GSGK-PPRAGEVSGGHGQ------SEFCFG-MS--DAKQAPKARGGN--------ASRRR +NGQKQKLSS-KHDVSSGDEMPRP-------------HAAV +>gnl_Carpa1.181_PACid_16420351 +---MADG------------------------------------------------EDKNN +SDLYAVLGLNKECTPAELRNAYKKLAMRWHPDRCSASG---NSMFVEEAKKKFQAIQEAY +S------VLSDANKRFLYDVGAYES--------DDDENGMGDFLNEMAAMMSQTKPNENG +NAQESFEELQ------ELFQEMFQGDMGFNT----------FGSSSQP------------ +----TTSSCSASSA------------------YATCSETSN-------PNNNKRNSS-EM +NYGK-KKVDDSSGFHAHF------QTFCLG-VE--QQQDFKKGKEARGGIRGKP-GGSRR +QGRKQKVSS-RHNVSSND-LGISAS--------------- +>gnl_Frave2.0_gene05408 +---MAGGKWVPPPLSQFHLHIKRFRRRQKVSGSSGNTEPSGYTDCKNISNR---RMEEKG +NDFYAVMGLKKECSDSELRNAYKKLALIWHPDRCSASG---NSKFVEEAKKKFQDIQQAY +S------VLSDANKRFLYDVGAYES--------DDDENGMGDFLNEMAVMMSQTKPNENG +--GESFEQLQ------ELFEEMFQGDI--EG----------FSSCSQP------------ +----PTSCSTSSSS------------------YALYCENST--------PSNKRNSS-AM +NYGN--ATLDSSGFDAHF------HNFCVG-T-----------GGKPAKDREGD-ARKRK +DSRRSNR--------------------------------- +>gnl_Mimgu1.0_PACid_17694730 +---MAAD-------------------------------------------------EEKS +SDFYGVLGLRKECTAAELRVAYKKLAMKWHPDRCSASG---NLKYVEEAKNKFQAVQQAY +S------VLSDANKRFLYDVGIYDSE------DDADENGMGDFLNEMVAMMGQSKPNENK +--NESFQELQ------DLFEEIFNNDA--EEV---------FKIPPPH------------ +--FPYQDSCSETRT-----------------------------------ASNKRNAR-EM +GSVN-----FSNIEATPF------EGFCIG-ENVIFGGERIQTRPG---------GGSRR +T--KPKIST-SID-----------------------GLIS +>gnl_Nelnu1.0_NNU_010544-RA +------------------------------------------------------------ +---------------------MNLLLQKWHPDRCSSSG---NSKFVEDSKKKFQAIQEAY +S------VLSDENKRFLYDVGVYDCDD-----DDDDENGMGEFLGEMATMMSQIKPSENG +--PESLEKLQ------ELFEEMFQRDM--DDG---------FFSPSPQCA---------- +---SFSSSCSSSSS---------------STTYFSYNNNKH---------DNKRNCS-DI +SSMD--DFYTFGTDSIQF------SNFCIG-VE--GGE-DSKVRGGK---------SRRK +SNRRQKVSSSKHDPSCR----------------------- +>gnl_Solly2.3_Solyc03g123560.2.1 +---M----------------------------------------------------EDKS +NDYYAVLGLKKECTDTELRNAYKKLALKWHPDRCSASG---NLKFVDEAKKQFQAIQEAY +S------VLSDANKKFLYDVGVYDSG------DDDDENGMGDFLNEMAAMMSQNKSNENQ +-GEETFEELQ------DMFNEMFNSDN--GT----------FSSSSS------------- +----SSSSWTGTPS------------------MCSTTSSTSSSET-FLTFPNKRSSG-EM +KSGS-----SVRGDSCQF------QGFCVG-A-----------GGTSGKCNERE-RSWRK +NSKSGRKH-------------------------------- +>gnl_Sorbi1.4_PACid_1968370 +---MDAGG-------------------------------------EKFSDAAAAEGGEGG +GDLYAVLGLKKECSDADLKVAYRKLAKKWHPDKCSSSS---SVKHMEEAKEKFQEIQGAY +S------VLSDANKRLLYDVGVYDDED-----DEDSMQGMGDFIGEMAQMMSQVRPTR-- +--QESFEELQ------QLFVDMFQSDI--DSG---------FCNGSAK-DQVQGQAKSRT +CSTSPSSSPSPPPP----------------PTIVKEAEVSS------CNGFNKRGSS-AM +DSGK-PPRP--VEGGAGQ------AGFCFG-VS--DTKQTPKPRGPN--------TSRRR +NGRKQKLSS-KHDVSSEDETAGS----------------- +>gnl_Thepa2.0_Tp3g12470 +---MASNN-----------------------------------------------SEKGN +DDLYGVLGLKKECTTTELRTAYKKLALRWHPDRCSSMG---TPEFVDEAKKKFQAIQEAY +S------VLSDSNKRFLYDVGAYNS-------DDEDQNGMGDFLNEMAAMMNQSKPSENN +-SGDSFEQLQ------DLFNEMFQGDA--AA----------FSSSSS------------- +------SSCSASTF------------------TSSCSFVFD--------TNSQRSPF-ET +SSMG---TNDLFGFDHSA------HTFSLG-VE--HQQDFKKGKN----------SGGRR +NRRKNNAQSAAHETASSNNYGVPTS--------------- +>gnl_Theca1.0_Tc06_g010450 +---MANG-------------------------------------------------EEKN +NDFYAVLGLNKECTPTELRTAYKKLALRWHPDRCSASG---NSKFVEEAKKKFQAIQQAY +S------VLSDSNKRFLYDVGAYDS--------DDDENGMGDFLNEMAGMMSQTKSNENG +--GESFEELQ------ELFEEMFQADI--DS----------FESTGQ------------- +----STPSCSASSS------------------FGSYGESSS---------SNKRNSS-EM +SSVE-TRLESSSSFDAQF------HSFCLG-VE--HRQDIKQHRGARGGMRGAAGGSRRR +NGRKQKVSS-GHDVTSND-CGISAS--------------- +>gnl_Vitvi12X_PACid_17827068 +---MAAG-------------------------------------------------EEKS +NDFYAVLGLKKECTASELRNAYKRLALMWHPDRCSSSG---NSKFVEEAKKKFQAIQEAY +S------VLSDANKRFLYDVGAYDS--------DDDENGMGDFLNEMAVMMSQTKSNENG +--KESFEELQ------ELFEDMFQRDV--DA----------FNSASHH------------ +----PMNSFPSSTS------------------TSSYCESSN--------ANNKRNSA-EM +GSGRMMSAGESSAFDAHF------QSFCFG-T-----------GGTPGRFQEGE-RSKRR +NSRRSQR--------------------------------- +>gnl_Selmo1.0_PACid_15401289 +---M----------------------------------------------------EKRK +EDPYTVLGVQKSSSSSEIRSAYRKLAMKWHPDK--------QHSLEDQAKAKFQGIQEAY +S------VLSDDKKRVLYDSGLYDEG------DDE------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------VS--------------------------- +---------------------------------------- +>gnl_Orysa6.0_PACid_16864430 +---MARGGG-----------------------------------G----------GGGAD +ADLYAVLGLSRECTDADLRLAYRKLAMIWHPDRCSVAGGSASAAGVDEAKERFQEIQGAY +S------VLSDSNKRFLYDVGVYDGNDGDDDDDEADLSGMGDFLGEMAQMMSQATP---- +--AESFEELQ------QLFVDMFQDDI--DAG---------LCQSTP------------- +----PPPSWPSPPA-------------------AANARSPAAAAT-SRKGVNKRCSP-AA +MDMD-----SGLSSLLGI------SGFCFE-AP--WTSQDASTAAGGG-------GGKRR +KQRPPPA---SHNV-------------------------- +>gnl_Sorbi1.4_PACid_1982925 +---MAATSH-----------------------------------CGNIQDQDEEASAPGA +ADLYAVLGLNRECTDAELRVAYRRLAMIWHPDRCSASG--SSPARMEEAKERFQEIQGAY +S------VLSDSNKRLLYDVGVYDSDD-----DEADLSGMGDFLGEMADMMSQATP---- +--TETFEELQ------QVFVDMFQDDLD-DAG---------FFGGLPT-TGRRAQA--PS +TSLPPSVSSSPLRP----------------TPAAGRSKGPQATPSSSFKGVERRGST-ST +AKRPRPNGSAGLESDLGL------SGFCFM-VS--KEMSKSKERQAV---WASD-DGDRS +TDGKQRLST-SRDVSGGG-MSRSLQGQSSKNLLQCMASKS +>gnl_Medtr3.5_Medtr8g022310.3 +---MANE-------------------------------------------------GNKS +NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY +S------VLSDSNKRLMYDVGVYDS--------DDDENVRHLF----------------- +---HTIHELG------TLFCVMFCFFISLR------------GE---------------- +---------KRSNL------------------NLTFSLSH-------------------- +------------------------------------------------------------ +---------------------------------------- +>gnl_Nelnu1.0_NNU_000115-RA +---MEVD------------------------------------------------SHRSS +PSYYTILGVDQNSSASEIRNAYRKLAMQWHPDKWTKTP-----SLLEKAKSKFQQIQEAY +SGGLLVFMLSDQGKRTLYDVGLYDPDD-----ETNDEVGLRRF--HAGDDISHERC---- +--EETGEEIQLGGTTGDVSGNVTRAGV--EDGECWWCVVVRWSCSLKE------------ +----------------------------------------------------------EL +KEGQ--------------------MGIISE-SD--DA----------------------- +----------GHDTPSLPHLHGSEL-----ELLGRTGCCN +>contig_7 +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------ENEWSGAEFLNEMAAMMTQNKSNENG +--TGTFEELQ------QLFDEMFQSDI--ES----------FNGCSSS------------ +----SNETCS---------------------------------------NSNKRNSI-ES +SSAN----------------FRPENGNESG-----------------------E-ISGKK +NTRKGKGDX-------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3722.faa.aln.tree Mon Oct 30 09:05:37 2017 -0400 @@ -0,0 +1,1 @@ +(((((gnl_Glyma1.01_PACid_16301085:0.016443402,gnl_Glyma1.01_PACid_16301084:0.053278093)0.803:0.023390563,gnl_Glyma1.01_PACid_16301083:0.030298601)0.901:0.027099626,((gnl_Glyma1.01_PACid_16266209:0.056847680,gnl_Glyma1.01_PACid_16266210:0.015624714)0.811:0.025333131,gnl_Glyma1.01_PACid_16266208:0.034488143)0.905:0.035494603)0.999:0.188079149,(gnl_Medtr3.5_Medtr8g022310.2:0.024981315,(gnl_Medtr3.5_Medtr8g022310.3:0.465525159,gnl_Medtr3.5_Medtr8g022310.1:0.036690818)0.074:0.002229085)0.952:0.101287628)1.000:0.225059008,(((((gnl_Orysa6.0_PACid_16843526:0.000000007,gnl_Orysa6.0_PACid_16843528:0.000000007)0.960:0.104692276,(gnl_Bradi1.2_Bradi3g60090.1:0.251215525,gnl_Sorbi1.4_PACid_1968370:0.202676729)0.470:0.035571250)0.964:0.220529391,(gnl_Orysa6.0_PACid_16864430:0.468545028,gnl_Sorbi1.4_PACid_1982925:0.504608123)0.995:0.341396682)0.999:0.333764302,((gnl_Musac1.0_GSMUA_Achr6T31040_001:0.257705603,gnl_Musac1.0_GSMUA_Achr9T18140_001:0.233035596)0.837:0.090223569,(gnl_Musac1.0_GSMUA_Achr8T23700_001:0.288734161,gnl_Musac1.0_GSMUA_AchrUn_randomT02210_001:0.550828541)0.916:0.084755065)0.866:0.093086055)0.999:0.343576670,(((gnl_Mimgu1.0_PACid_17694730:0.627920829,((gnl_Soltu3.4_PGSC0003DMP400016106:0.060397140,(gnl_Soltu3.4_PGSC0003DMP400016105:0.000000007,gnl_Solly2.3_Solyc03g123560.2.1:0.117851013)0.917:0.075604816)0.676:0.104109587,(gnl_Selmo1.0_PACid_15401289:0.393757146,gnl_Nelnu1.0_NNU_000115-RA:1.006137326)0.989:1.057259060)0.804:0.231585972)0.632:0.070827174,(gnl_Nelnu1.0_NNU_010544-RA:0.445330506,(gnl_Ambtr1.0.27_AmTr_v1.0_scaffold00007.329:0.481404311,gnl_Aquco1.0_PACid_18141277:0.569001355)0.869:0.111238919)0.913:0.101469446)0.876:0.061617758,(gnl_Frave2.0_gene05408:0.298252983,gnl_Vitvi12X_PACid_17827068:0.183978617)0.975:0.124539672)0.258:0.016419054)0.666:0.050639012,(((contig_7:0.847311108,gnl_Theca1.0_Tc06_g010450:0.107098111)0.806:0.076702503,((gnl_Arath10_AT3G14200.1:0.118641618,gnl_Thepa2.0_Tp3g12470:0.089890295)1.000:0.506633729,gnl_Carpa1.181_PACid_16420351:0.140839270)0.773:0.074226625)0.858:0.037834597,(gnl_Poptr2.2_PACid_18217800:0.237912037,(gnl_Poptr2.2_PACid_18234651:0.048333265,(gnl_Poptr2.2_PACid_18234649:0.000000007,gnl_Poptr2.2_PACid_18234650:0.000000007)0.962:0.063277271)0.890:0.133521212)0.996:0.168273995)0.846:0.051958868);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tool-data/plant_tribes/scaffolds/README.txt Mon Oct 30 09:05:37 2017 -0400 @@ -0,0 +1,3 @@ +For functional tests to work, this directory must contain symlinks to the scaffolds data +installed into the Galaxy instance to which planemo points via the --galaxy_root parameter. +This would typically be something like ~/galaxy/tool-data/plant_tribes/scaffolds/22Gv1.1.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon Oct 30 09:05:37 2017 -0400 @@ -0,0 +1,6 @@ +<tables> + <table name="plant_tribes_scaffolds" comment_char="#"> + <columns>value, name, path, description</columns> + <file path="${__HERE__}/plant_tribes_scaffolds.loc" /> + </table> +</tables>
--- a/utils.py Wed Oct 25 11:30:45 2017 -0400 +++ b/utils.py Mon Oct 30 09:05:37 2017 -0400 @@ -54,29 +54,3 @@ def stop_err(msg): sys.exit(msg) - - -def write_html_output(output, title, dir): - with open(output, 'w') as fh: - dir_items = sorted(os.listdir(dir)) - # Directories can only contain either files or directories, - # but not both. - if len(dir_items) > 0: - item_path = os.path.join(dir, dir_items[0]) - if os.path.isdir(item_path): - header = 'Directories' - else: - header = 'Datasets' - else: - header = '' - fh.write('<html><head><h3>%s: %d items</h3></head>\n' % (title, len(dir_items))) - fh.write('<body><p/><table cellpadding="2">\n') - fh.write('<tr><b>%s</th></b>\n' % header) - for index, fname in enumerate(dir_items): - if index % 2 == 0: - bgcolor = '#D8D8D8' - else: - bgcolor = '#FFFFFF' - link = '<a href="%s" type="text/plain">%s</a>\n' % (fname, fname) - fh.write('<tr bgcolor="%s"><td>%s</td></tr>\n' % (bgcolor, link)) - fh.write('</table></body></html>\n')