| Previous changeset 10:79ea0eef1942 (2018-09-04) |
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Commit message:
planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/gene_family_aligner commit f7690d10e0515911ee00455806e457bc53f145c7-dirty |
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modified:
gene_family_aligner.xml macros.xml |
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removed:
.shed.yml test-data/3722.faa.aln test-data/3722.fna.aln test-data/38889.faa.aln test-data/38889.fna.aln test-data/39614.faa.aln test-data/39614.fna.aln utils.py |
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| diff -r 79ea0eef1942 -r 1c5a484fc06f .shed.yml --- a/.shed.yml Tue Sep 04 08:51:38 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,13 +0,0 @@ -name: plant_tribes_gene_family_aligner -owner: greg -description: | - Contains a tool that integrates de novo assembly sequences with scaffold gene family sequences. -homepage_url: https://github.com/dePamphilis/PlantTribes -long_description: | - Contains a tool that tool is one of the PlantTribes collection of automated modular analysis pipelines that - utilize objective classifications of complete protein sequences from sequenced plant genomes to perform - comparative evolutionary studies. This tool aligns gene family sequences. -remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/gene_family_aligner -type: unrestricted -categories: -- Phylogenetics |
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| diff -r 79ea0eef1942 -r 1c5a484fc06f gene_family_aligner.xml --- a/gene_family_aligner.xml Tue Sep 04 08:51:38 2018 -0400 +++ b/gene_family_aligner.xml Thu Jun 13 11:54:31 2024 +0000 |
| [ |
| b'@@ -1,10 +1,10 @@\n-<tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.3.0">\n+<tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@TOOL_VERSION@.4.0+galaxy0">\n <description>aligns integrated orthologous gene family clusters</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n <requirements>\n- <requirement type="package" version="1.0.3">plant_tribes_gene_family_aligner</requirement>\n+ <requirement type="package" version="1.0.4">plant_tribes_gene_family_aligner</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n #set alignment_method = $alignment_method_cond.alignment_method\n@@ -138,7 +138,7 @@\n </collection>\n </outputs>\n <tests>\n- <test>\n+ <test expect_num_outputs="2">\n <param name="input">\n <collection type="list">\n <element name="3722.faa" value="3722.faa"/>\n@@ -151,14 +151,62 @@\n </param>\n <param name="codon_alignments" value="yes"/>\n <output_collection name="primary_faa" type="list">\n- <element name="3722.faa.aln" file="3722.faa.aln" ftype="fasta"/>\n- <element name="38889.faa.aln" file="38889.faa.aln" ftype="fasta"/>\n- <element name="39614.faa.aln" file="39614.faa.aln" ftype="fasta"/>\n+ <element name="3722.faa.aln" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">gnl_Glyma1.01_PACid_16266208"/>\n+ <has_text text=">gnl_Vitvi12X_PACid_17827068"/>\n+ <has_text text=">gnl_Selmo1.0_PACid_15401289"/>\n+ <has_text text=">gnl_Orysa6.0_PACid_16864430"/>\n+ <has_text text=">contig_7"/>\n+ </assert_contents>\n+ </element>\n+ <element name="38889.faa.aln" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">gnl_Mimgu1.0_PACid_17675619"/>\n+ <has_text text=">gnl_Solly2.3_Solyc06g053200.2.1"/>\n+ <has_text text=">gnl_Mimgu1.0_PACid_17675619"/>\n+ <has_text text=">gnl_Solly2.3_Solyc06g053200.2.1"/>\n+ <has_text text=">contig_2"/>\n+ </assert_contents>\n+ </element>\n+ <element name="39614.faa.aln" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">gnl_Orysa6.0_PACid_16878968"/>\n+ <has_text text=">gnl_Phoda3.0_PDK_30s1023721g001"/>\n+ <has_text text=">gnl_Orysa6.0_PACid_16878968"/>\n+ <has_text text=">gnl_Phoda3.0_PDK_30s1023721g001"/>\n+ <has_text text=">contig_3"/>\n+ </assert_contents>\n+ </element>\n </output_collection>\n <output_collection name="primary_fna" type="list">\n- <element name="3722.fna.aln" file="3722.fna.aln" ftype="fasta"/>\n- <element name="38889.fna.aln" file="38889.fna.aln" ftype="fasta"/>\n- <element name="39614.fna.aln" file="39614.fna.aln" ftype="fasta"/>\n+ <element name="3722.fna.aln" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">gnl_Glyma1.01_PACid_16266208"/>\n+ <has_text text=">gnl_Glyma1.01_PACid_16266209"/>\n+ <has_text text=">gnl_Glyma1.01_PACid_16266210"/>\n+ <has_text text=">gnl_Glyma1.01_PACid_16301083"/>\n+ <has_text text=">contig_7"/>\n+ </assert_contents>\n+ </element>\n+ <element name="38889.fna.aln" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">gnl_Mimgu1.'..b'fna.aln" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">gnl_Orysa6.0_PACid_16878968"/>\n+ <has_text text=">gnl_Phoda3.0_PDK_30s1023721g001"/>\n+ <has_text text=">gnl_Orysa6.0_PACid_16878968"/>\n+ <has_text text=">gnl_Phoda3.0_PDK_30s1023721g001"/>\n+ <has_text text=">contig_3"/>\n+ </assert_contents>\n+ </element>\n </output_collection>\n </test>\n </tests>\n@@ -199,65 +247,16 @@\n \n </help>\n <citations>\n- <expand macro="citation1" />\n- <citation type="bibtex">\n- @article{Wall2008,\n- journal = {Nucleic Acids Research},\n- author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS},\n- title = {PlantTribes: a gene and gene family resource for comparative genomics in plants},\n- year = {2008},\n- volume = {36},\n- number = {suppl 1},\n- pages = {D970-D976},}\n- </citation>\n- <citation type="bibtex">\n- @article{Katoh2013,\n- journal = {Molecular biology and evolution},\n- author = {3. Katoh K, Standley DM},\n- title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},\n- year = {2013},\n- volume = {30},\n- number = {4},\n- pages = {772-780},}\n- </citation>\n- <citation type="bibtex">\n- @article{Mirarab2014,\n- journal = {Research in Computational Molecular Biology (RECOMB)},\n- author = {4. Mirarab S, Nguyen N, Warnow T},\n- title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan (Ed.)},\n- year = {2014},\n- pages = {177\xe2\x80\x93191},\n- url = {https://github.com/smirarab/pasta},}\n- </citation>\n- <citation type="bibtex">\n- @article{Capella-Gutierrez2009,\n- journal = {Bioinformatics,},\n- author = {5. Capella-Gutierrez S, Silla-Mart\xc3\xadnez JM, Gabald\xc3\xb3n T},\n- title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},\n- year = {2009},\n- volume = {25},\n- number = {15},\n- pages = {1972-1973},}\n- </citation>\n- <citation type="bibtex">\n- @article{Yachdav2016,\n- journal = {Bioinformatics,},\n- author = {6. Yachdav G, Wilzbach S, Rauscher B, Sheridan R, Sillitoe I, Procter J, Lewis SE, Rost B, Goldberg T},\n- title = {MSAViewer: interactive JavaScript visualization of multiple sequence alignments},\n- year = {2016},\n- volume = {32},\n- number = {22},\n- pages = {3501-3503},}\n- </citation>\n- <citation type="bibtex">\n- @article{Clamp2004,\n- journal = {Bioinformatics,},\n- author = {7. Clamp M, Cuff J, Searle SM, Barton GJ},\n- title = {The jalview java alignment editor},\n- year = {2004},\n- volume = {20},\n- number = {3},\n- pages = {426-427},}\n- </citation>\n+ <citation type="doi">10.3389/fpls.2022.1011199</citation>\n+ <citation type="doi">10.1371/journal.pone.0146062</citation>\n+ <citation type="doi">10.1038/nprot.2013.084</citation>\n+ <citation type="doi">10.1101/gr.9.9.868</citation>\n+ <citation type="doi">10.1142/9781848165632_0019</citation>\n+ <citation type="doi">10.1093/molbev/mst010</citation>\n+ <citation type="doi">10.1093/nar/gks631</citation>\n+ <citation type="doi">10.1101/gr.1224503</citation>\n+ <citation type="doi">10.1186/s13059-015-0721-2</citation>\n+ <citation type="doi">10.1093/bioinformatics/btp348</citation>\n+ <citation type="doi">10.1109/TCBB.2013.68</citation>\n </citations>\n </tool>\n' |
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| diff -r 79ea0eef1942 -r 1c5a484fc06f macros.xml --- a/macros.xml Tue Sep 04 08:51:38 2018 -0400 +++ b/macros.xml Thu Jun 13 11:54:31 2024 +0000 |
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| @@ -1,28 +1,4 @@ <?xml version='1.0' encoding='UTF-8'?> <macros> - <token name="@WRAPPER_VERSION@">1.0</token> - <xml name="param_method"> - <param name="method" type="select" label="Protein clustering method" dynamic_options="get_clustering_method_options(scaffold)"/> - </xml> - <xml name="param_scaffold"> - <param name="scaffold" type="select" label="Gene family scaffold" refresh_on_change="True"> - <options from_data_table="plant_tribes_scaffolds"> - <column name="name" index="1"/> - <column name="value" index="2"/> - <column name="path" index="2"/> - <filter type="sort_by" column="1"/> - <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table."/> - </options> - </param> - </xml> - <xml name="citation1"> - <citation type="bibtex"> - @misc{None, - journal = {None}, - author = {1. Wafula EK}, - title = {Manuscript in preparation}, - year = {None}, - url = {https://github.com/dePamphilis/PlantTribes},} - </citation> - </xml> + <token name="@TOOL_VERSION@">1.0</token> </macros> |
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| diff -r 79ea0eef1942 -r 1c5a484fc06f test-data/3722.faa.aln --- a/test-data/3722.faa.aln Tue Sep 04 08:51:38 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,312 +0,0 @@\n->gnl_Glyma1.01_PACid_16266208\n----MANE-------------------------------------------------GKKS\n-NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY\n-S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG\n---EESFEELQ------QLFEDMFQADI--GL----------DGGPSL-------------\n-----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM\n-NFGK---AENSSVFDASY------QNFCFG-VN--QLQDIKKGK---GGILGGGGRSRHR\n-SGRKQKMFY-GHDV--------------------------\n->gnl_Glyma1.01_PACid_16266209\n----MANE-------------------------------------------------GKKS\n-NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY\n-S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG\n---EESFEELQ------QLFEDMFQADI--GL----------DGGPSL-------------\n-----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM\n-NFGK---AENSSVFDASY------QNFCFG-TG--EPTPRYKEG--------KGGNSRRR\n-R---------------------------------------\n->gnl_Glyma1.01_PACid_16266210\n----MANE-------------------------------------------------GKKS\n-NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY\n-S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG\n---EESFEELQ------QLFEDMFQADI--GL----------DGGPSL-------------\n-----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM\n-NFGK---AENSSVFDASY------QNFCFG-VG--HVNYHYQ------------------\n-----------------------------------------\n->gnl_Glyma1.01_PACid_16301083\n----MADE-------------------------------------------------GNKS\n-NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY\n-S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG\n---EESFEELQ------QLFEDMFEADI--GL----------DGGPSL-------------\n-----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM\n-NFGK---AENSSVFDAGY------QNFCFG-VN--QLQDIKKKK---GGIL-GGGRSRHR\n-NGRKQNMSY-GHDVSSNDYPGISTK---------------\n->gnl_Glyma1.01_PACid_16301085\n----MADE-------------------------------------------------GNKS\n-NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY\n-S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG\n---EESFEELQ------QLFEDMFEADI--GL----------DGGPSL-------------\n-----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM\n-NFGK---AENSSVFDAGY------QNFCFG-VG--HVNYHYQ------------------\n-----------------------------------------\n->gnl_Glyma1.01_PACid_16301084\n----MADE-------------------------------------------------GNKS\n-NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY\n-S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG\n---EESFEELQ------QLFEDMFEADI--GL----------DGGPSL-------------\n-----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM\n-NFGK---AENSSVFDAGY------QNFCFG-TG--EPTPRYKEE--------KGGNSRRR\n-----------------------------------------\n->gnl_Medtr3.5_Medtr8g022310.1\n----MANE-------------------------------------------------GNKS\n-NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY\n-S------VLSDSNKRLMYDVGVYDS--------DDDENGMGDFLNEMVTMMSQTKSNENG\n---EESFEELQ------QLFDDMFQADI--GL----------NGSTSL-------------\n-----NASGCSTSST------------------FMTFSESSN---------SNKRNST-QM\n-NFGK---AEDSSSFGANY------QNFCFG-MK--HLQEDVEKE--KGGILEGGGSKKQR\n-KGRKQKISC-GH-VSSNDHPGISAN---------------\n->gnl_Medtr3.5_Medtr8g022310.2\n----MANE-------------------------------------------------GNKS\n-NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY\n-S------VLSDSNKRLMYDVGVYDS--------DDDENGMGDFLNEMVTMMSQTKSNENG\n---EESFEELQ------QLFDDMFQADI--GL----------NGSTSL-------------\n-----NASGCSTSST------------------FMTFSESSN---------SNKRNST-QM\n-NFGK---AEDSSSFGANY------QNFCFG-VN--LVNYHYQ------------------\n-----------------------------------------\n->gnl_Musac1.0_GSMUA_Achr6T31040_001\n----MAAE-------------------------------------------------EDKS\n-GDFYAVLGLRKECSETELRNAYKKLAMRWHPDKCLASG---NAQIVGEAKEKFQEIQKAY\n-S------VLSDSNKRFLYDVGVYDND------DDNDENGMGDFIGEMLEMMSQTKPNENS\n---QDSFQELQ------ELFVEMFQDDL--DAG---------FGGSIFH-DCPWAQP----\n----TNGQDCWTSSG------------------LHFANGRSK--------CGNKRGNS-AV\n-NLGK----VNLEELEHGT------SDFYFG-LN--DAAQPSQGKGGS--------NNKRR\n-NGRKQKVSS-N'..b'HDVSSEDETAGS-----------------\n->gnl_Thepa2.0_Tp3g12470\n----MASNN-----------------------------------------------SEKGN\n-DDLYGVLGLKKECTTTELRTAYKKLALRWHPDRCSSMG---TPEFVDEAKKKFQAIQEAY\n-S------VLSDSNKRFLYDVGAYNS-------DDEDQNGMGDFLNEMAAMMNQSKPSENN\n--SGDSFEQLQ------DLFNEMFQGDA--AA----------FSSSSS-------------\n-------SSCSASTF------------------TSSCSFVFD--------TNSQRSPF-ET\n-SSMG---TNDLFGFDHSA------HTFSLG-VE--HQQDFKKGKN----------SGGRR\n-NRRKNNAQSAAHETASSNNYGVPTS---------------\n->gnl_Theca1.0_Tc06_g010450\n----MANG-------------------------------------------------EEKN\n-NDFYAVLGLNKECTPTELRTAYKKLALRWHPDRCSASG---NSKFVEEAKKKFQAIQQAY\n-S------VLSDSNKRFLYDVGAYDS--------DDDENGMGDFLNEMAGMMSQTKSNENG\n---GESFEELQ------ELFEEMFQADI--DS----------FESTGQ-------------\n-----STPSCSASSS------------------FGSYGESSS---------SNKRNSS-EM\n-SSVE-TRLESSSSFDAQF------HSFCLG-VE--HRQDIKQHRGARGGMRGAAGGSRRR\n-NGRKQKVSS-GHDVTSND-CGISAS---------------\n->gnl_Vitvi12X_PACid_17827068\n----MAAG-------------------------------------------------EEKS\n-NDFYAVLGLKKECTASELRNAYKRLALMWHPDRCSSSG---NSKFVEEAKKKFQAIQEAY\n-S------VLSDANKRFLYDVGAYDS--------DDDENGMGDFLNEMAVMMSQTKSNENG\n---KESFEELQ------ELFEDMFQRDV--DA----------FNSASHH------------\n-----PMNSFPSSTS------------------TSSYCESSN--------ANNKRNSA-EM\n-GSGRMMSAGESSAFDAHF------QSFCFG-T-----------GGTPGRFQEGE-RSKRR\n-NSRRSQR---------------------------------\n->gnl_Selmo1.0_PACid_15401289\n----M----------------------------------------------------EKRK\n-EDPYTVLGVQKSSSSSEIRSAYRKLAMKWHPDK--------QHSLEDQAKAKFQGIQEAY\n-S------VLSDDKKRVLYDSGLYDEG------DDE-------------------------\n-------------------------------------------------------------\n-------------------------------------------------------------\n--------------------------------VS---------------------------\n-----------------------------------------\n->gnl_Orysa6.0_PACid_16864430\n----MARGGG-----------------------------------G----------GGGAD\n-ADLYAVLGLSRECTDADLRLAYRKLAMIWHPDRCSVAGGSASAAGVDEAKERFQEIQGAY\n-S------VLSDSNKRFLYDVGVYDGNDGDDDDDEADLSGMGDFLGEMAQMMSQATP----\n---AESFEELQ------QLFVDMFQDDI--DAG---------LCQSTP-------------\n-----PPPSWPSPPA-------------------AANARSPAAAAT-SRKGVNKRCSP-AA\n-MDMD-----SGLSSLLGI------SGFCFE-AP--WTSQDASTAAGGG-------GGKRR\n-KQRPPPA---SHNV--------------------------\n->gnl_Sorbi1.4_PACid_1982925\n----MAATSH-----------------------------------CGNIQDQDEEASAPGA\n-ADLYAVLGLNRECTDAELRVAYRRLAMIWHPDRCSASG--SSPARMEEAKERFQEIQGAY\n-S------VLSDSNKRLLYDVGVYDSDD-----DEADLSGMGDFLGEMADMMSQATP----\n---TETFEELQ------QVFVDMFQDDLD-DAG---------FFGGLPT-TGRRAQA--PS\n-TSLPPSVSSSPLRP----------------TPAAGRSKGPQATPSSSFKGVERRGST-ST\n-AKRPRPNGSAGLESDLGL------SGFCFM-VS--KEMSKSKERQAV---WASD-DGDRS\n-TDGKQRLST-SRDVSGGG-MSRSLQGQSSKNLLQCMASKS\n->gnl_Medtr3.5_Medtr8g022310.3\n----MANE-------------------------------------------------GNKS\n-NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY\n-S------VLSDSNKRLMYDVGVYDS--------DDDENVRHLF-----------------\n----HTIHELG------TLFCVMFCFFISLR------------GE----------------\n----------KRSNL------------------NLTFSLSH--------------------\n-------------------------------------------------------------\n-----------------------------------------\n->gnl_Nelnu1.0_NNU_000115-RA\n----MEVD------------------------------------------------SHRSS\n-PSYYTILGVDQNSSASEIRNAYRKLAMQWHPDKWTKTP-----SLLEKAKSKFQQIQEAY\n-SGGLLVFMLSDQGKRTLYDVGLYDPDD-----ETNDEVGLRRF--HAGDDISHERC----\n---EETGEEIQLGGTTGDVSGNVTRAGV--EDGECWWCVVVRWSCSLKE------------\n-----------------------------------------------------------EL\n-KEGQ--------------------MGIISE-SD--DA-----------------------\n-----------GHDTPSLPHLHGSEL-----ELLGRTGCCN\n->contig_7\n-------------------------------------------------------------\n-------------------------------------------------------------\n-----------------------------------ENEWSGAEFLNEMAAMMTQNKSNENG\n---TGTFEELQ------QLFDEMFQSDI--ES----------FNGCSSS------------\n-----SNETCS---------------------------------------NSNKRNSI-ES\n-SSAN----------------FRPENGNESG-----------------------E-ISGKK\n-NTRKGKGDX-------------------------------\n' |
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| diff -r 79ea0eef1942 -r 1c5a484fc06f test-data/3722.fna.aln --- a/test-data/3722.fna.aln Tue Sep 04 08:51:38 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,819 +0,0 @@\n->gnl_Glyma1.01_PACid_16266208\n----------ATGGCTAATGAA---------------------------------------\n-------------------------------------------------------------\n-------------------------------------------------GGAAAGAAAAGC\n-AATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAAGAAT\n-GCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGG------\n----AATTTAGAGTTAGTGGAAGAAGCTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTAT\n-TCT------------------GTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTG\n-GGAGTCTACGACAGT------------------------GATGACGACGAAAACGGCATG\n-GGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATCAAATGAAAATGGA\n-------GAGGAGAGCTTTGAGGAGTTGCAA------------------CAGCTTTTTGAA\n-GACATGTTTCAAGCGGATATT------GGATTG---------------------------\n----GATGGAGGCCCTTCTCTT---------------------------------------\n-------------GCTTCTTCTGATTCCTCAACTTCATCTGCT------------------\n-------------------------------------TACATGACTTACAGTGAAAGTTCT\n-AGT---------------------------TCAAATAAACGCAATTCCTCT---GAGATG\n-AATTTCGGGAAG---------GCAGAGAATTCTTCTGTCTTTGATGCCAGTTAC------\n-------------CAGAATTTCTGTTTTGGG---GTGAAC------CAACTCCAAGATATA\n-AAGAAGGGAAAG---------GGGGGAATTCTAGGAGGAGGAGGTAGAAGTAGACACAGA\n-AGTGGCAGAAAGCAAAAAATGTTCTAT---GGCCATGATGTT------------------\n-------------------------------------------------------------\n->gnl_Glyma1.01_PACid_16266209\n----------ATGGCTAATGAA---------------------------------------\n-------------------------------------------------------------\n-------------------------------------------------GGAAAGAAAAGC\n-AATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAAGAAT\n-GCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGG------\n----AATTTAGAGTTAGTGGAAGAAGCTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTAT\n-TCT------------------GTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTG\n-GGAGTCTACGACAGT------------------------GATGACGACGAAAACGGCATG\n-GGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATCAAATGAAAATGGA\n-------GAGGAGAGCTTTGAGGAGTTGCAA------------------CAGCTTTTTGAA\n-GACATGTTTCAAGCGGATATT------GGATTG---------------------------\n----GATGGAGGCCCTTCTCTT---------------------------------------\n-------------GCTTCTTCTGATTCCTCAACTTCATCTGCT------------------\n-------------------------------------TACATGACTTACAGTGAAAGTTCT\n-AGT---------------------------TCAAATAAACGCAATTCCTCT---GAGATG\n-AATTTCGGGAAG---------GCAGAGAATTCTTCTGTCTTTGATGCCAGTTAC------\n-------------CAGAATTTCTGTTTTGGG---ACAGGT------GAACCAACTCCAAGA\n-TATAAAGAAGGG------------------------AAAGGGGGGAATTCTAGGAGGAGG\n-AGG---------------------------------------------------------\n-------------------------------------------------------------\n->gnl_Glyma1.01_PACid_16266210\n----------ATGGCTAATGAA---------------------------------------\n-------------------------------------------------------------\n-------------------------------------------------GGAAAGAAAAGC\n-AATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAAGAAT\n-GCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGG------\n----AATTTAGAGTTAGTGGAAGAAGCTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTAT\n-TCT------------------GTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTG\n-GGAGTCTACGACAGT------------------------GATGACGACGAAAACGGCATG\n-GGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATCAAATGAAAATGGA\n-------GAGGAGAGCTTTGAGGAGTTGCAA------------------CAGCTTTTTGAA\n-GACATGTTTCAAGCGGATATT------GGATTG---------------------------\n----GATGGAGGCCCTTCTCTT---------------------------------------\n-------------GCTTCTTCTGATTCCTCAACTTCATCTGCT------------------\n-------------------------------------TACATGACTTACAGTGAAAGTTCT\n-AGT---------------------------TCAAATAAACGCAATTCCTCT---GAGATG\n-AATTTCGGGAAG---------GCAGAGAATTCTTCTGTCTTTGATGCCAGTTAC------\n-------------CAGAATTTCTGTTTTGGG---GTCGGT------CATGTAAACTATCAT\n-TACCAA------------------------------------------------------\n-------------------------------------------------------------\n-------------------------------------------------------------\n->gnl_Glyma1.01_PACid_16301083\n----------ATGGCCGATGAA---------------------------------------\n-------------------------------------------------------------\n-------------'..b'------AAGGAGATGAGCAAG\n-TCGAAGGAGAGGCAAGCGGTA---------TGGGCCAGTGAC---GACGGTGACAGGAGC\n-ACCGATGGCAAGCAGAGGTTGTCGACG---AGCCGCGATGTCTCCGGTGGTGGG---ATG\n-TCACGCTCACTGCAGGGCCAAAGCAGCAAAAACTTGTTGCAGTGTATGGCCTCTAAGTCT\n->gnl_Medtr3.5_Medtr8g022310.3\n----------ATGGCTAACGAA---------------------------------------\n-------------------------------------------------------------\n-------------------------------------------------GGAAACAAAAGC\n-AATGATTTCTATGCAGTTTTGGGATTGAATAAGGAATGCTCTGATTCAGAGCTAAGGAAT\n-GCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGTTGTTCAGCTTCAGGG------\n----AATGTGAAGTTTGTGGAAGAAGCTAAGAAGAAATTTCAGGCAATTCAAGAAGCCTAT\n-TCT------------------GTTTTATCTGACTCGAACAAGAGATTAATGTACGACGTT\n-GGAGTTTACGACAGT------------------------GATGATGACGAAAATGTAAGG\n-CACTTGTTT---------------------------------------------------\n----------CACACCATTCATGAGTTGGGG------------------ACCCTCTTTTGC\n-GTTATGTTTTGTTTCTTCATTTCCTTGAGG------------------------------\n-------GGAGAG------------------------------------------------\n----------------------------AAGAGAAGCAACCTT------------------\n-------------------------------------AATTTAACCTTTTCACTTTCACAT\n-------------------------------------------------------------\n-------------------------------------------------------------\n-------------------------------------------------------------\n-------------------------------------------------------------\n-------------------------------------------------------------\n-------------------------------------------------------------\n->gnl_Nelnu1.0_NNU_000115-RA\n----------ATGGAGGTGGAC---------------------------------------\n-------------------------------------------------------------\n----------------------------------------------TCCCATCGATCATCT\n-CCATCTTACTACACCATCCTTGGTGTAGATCAGAATTCCTCCGCTTCCGAGATACGCAAT\n-GCTTACAGGAAGCTCGCGATGCAATGGCATCCAGACAAATGGACGAAAACTCCG------\n----------TCGCTCTTAGAGAAAGCCAAGAGTAAATTCCAGCAAATCCAGGAGGCTTAT\n-TCGGGTGGGTTACTCGTTTTCATGTTATCGGATCAGGGGAAGAGAACACTGTATGATGTC\n-GGTCTGTATGACCCGGACGAT---------------GAAACGAATGACGAGGTGGGGCTT\n-CGCAGATTT------CATGCAGGAGATGATATCTCTCATGAACGATGT------------\n-------GAAGAAACAGGAGAAGAAATACAGCTTGGAGGAACTACAGGAGATGTTAGTGGA\n-AATGTCACAAGGGCTGGAGTT------GAAGATGGAGAGTGCTGGTGGTGTGTGGTTGTT\n-AGATGGAGCTGCAGCCTCAAGGAG------------------------------------\n-------------------------------------------------------------\n-------------------------------------------------------------\n-------------------------------------------------------GAGCTC\n-AAAGAGGGCCAG------------------------------------------------\n-------------ATGGGAATCATCAGCGAG---TCCGAC------GACGCT---------\n-------------------------------------------------------------\n-------------------------------GGACACGACACACCTTCTCTCCCCCACTTG\n-CACGGTTCAGAGCTG---------------GAATTGTTAGGAAGAACCGGCTGTTGCAAT\n->contig_7\n-------------------------------------------------------------\n-------------------------------------------------------------\n-------------------------------------------------------------\n-------------------------------------------------------------\n-------------------------------------------------------------\n-------------------------------------------------------------\n-------------------------------------------------------------\n-------------------------------------------GAGAATGAGTGGTCTGGG\n-GCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAATAAATCCAATGAAAACGGA\n-------ACCGGAACTTTTGAAGAACTGCAA------------------CAATTGTTCGAT\n-GAAATGTTTCAGAGCGACATC------GAGTCC---------------------------\n----TTCAATGGTTGTTCTTCATCA------------------------------------\n-------------TCCAATGAAACATGTAGC------------------------------\n-------------------------------------------------------------\n----------------------------AACTCGAACAAGAGGAATTCCATT---GAGTCG\n-AGCTCGGCTAAT------------------------------------------------\n-TTCAGACCCGAAAATGGAAACGAAAGCGGC------------------------------\n----------------------------------------GAG---ATTAGCGGGAAGAAG\n-AATACTAGGAAAGGTAAAGGTGACGNN---------------------------------\n-------------------------------------------------------------\n' |
| b |
| diff -r 79ea0eef1942 -r 1c5a484fc06f test-data/38889.faa.aln --- a/test-data/38889.faa.aln Tue Sep 04 08:51:38 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,18 +0,0 @@ ->gnl_Mimgu1.0_PACid_17675619 -MAETKTK--VLKFDAEEDVAVALAKYTAYLSEKYIKEKNSFSVVLSGGTLIDTLRKLVEF -PYKDSVDWSKWLIFWVDERVVPLDHEDSNYLLAYRGFLSKVPIPPSNIYAINDKKSPEGA -ADDYEERIKNLVEEKTLPISD-SGFPKFDLMLLGMGPDGHVASLFPSHNQRYEKKRWVTF -ITDSPKPPPPRITFTFPVINSASDIAMVVTGAELADTTKKALGNEKHTLP---PLPCTEV -SAERELTWFLDKDAASKL-------- ->gnl_Solly2.3_Solyc06g053200.2.1 -MATQKGKKTVLKFDSEEDVSKALAKYTAELSEKFIKQKGSFTVVLSGGSLIDTMRKLVEP -PYKDSIDWSKWWIFWVDERVVPLGHDDSNYKLASDGFLSKVPIPSSNIYAINDKESPEGA -AADYEARLKQLIESKVLPLSAITGFPKFDLMLLGMGPDGHVASLFPLHPHRHEKERLVTF -ITDSPKPPPPRITFTFPVINSASEIAMVVTGAELAHMVDVALGNAP--PPDGIPPPCTEV -SAEEELTWFLDKDAASEL----QTSR ->contig_2 ------------------------------------------------------------- -------------------------------------XLSKVPIPSNNIYAINDKKSPEDA -ADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKWVTF -ITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEV -SAEGEVTWFLDKDAASQLLNYVRFDD |
| b |
| diff -r 79ea0eef1942 -r 1c5a484fc06f test-data/38889.fna.aln --- a/test-data/38889.fna.aln Tue Sep 04 08:51:38 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,45 +0,0 @@ ->gnl_Mimgu1.0_PACid_17675619 -ATGGCCGAAACCAAAACAAAA------GTACTGAAATTCGACGCGGAGGAAGATGTGGCC -GTCGCTCTAGCAAAGTACACCGCCTATCTCTCCGAAAAGTACATCAAGGAAAAGAATTCT -TTCTCGGTGGTTCTCTCCGGCGGCACCCTAATAGATACACTCAGGAAACTAGTAGAGTTT -CCATACAAGGATTCTGTGGATTGGTCGAAATGGCTGATATTTTGGGTTGACGAGAGAGTG -GTTCCTCTTGATCATGAAGACAGCAACTACTTACTTGCATACCGTGGTTTTCTTTCAAAG -GTACCTATTCCTCCAAGCAACATTTACGCAATCAACGACAAGAAGTCTCCGGAAGGTGCA -GCCGATGATTACGAGGAGCGTATCAAGAATCTGGTCGAGGAAAAAACCCTACCTATTTCA -GAC---AGTGGCTTCCCTAAATTCGACCTTATGCTTCTCGGAATGGGGCCCGATGGCCAC -GTGGCGTCTCTTTTCCCCTCTCACAATCAACGGTACGAAAAGAAACGGTGGGTGACATTC -ATAACTGACTCTCCCAAACCGCCGCCACCTAGGATCACTTTCACATTCCCAGTCATCAAC -TCTGCTTCGGACATTGCAATGGTGGTCACTGGTGCTGAGCTGGCGGATACTACGAAGAAA -GCATTGGGAAACGAGAAGCATACTCTTCCT---------CCTCTTCCTTGTACTGAAGTT -TCGGCTGAGAGAGAGCTCACTTGGTTCTTGGACAAAGATGCTGCTTCTAAACTG------ ------------------- ->gnl_Solly2.3_Solyc06g053200.2.1 -ATGGCAACCCAGAAAGGGAAGAAGACGGTGCTAAAATTCGACTCCGAAGAAGATGTATCA -AAGGCACTTGCTAAATACACTGCTGAGCTATCGGAAAAATTCATCAAACAAAAAGGTTCT -TTCACTGTTGTGCTCTCTGGTGGTTCTCTTATCGATACCATGAGGAAATTGGTAGAGCCG -CCGTACAAAGACTCAATTGATTGGTCGAAATGGTGGATTTTTTGGGTAGACGAAAGAGTG -GTTCCTCTAGGTCACGATGATAGCAATTATAAACTTGCTTCGGATGGGTTTCTTTCTAAG -GTTCCGATCCCCTCTTCTAACATTTATGCGATTAATGACAAGGAGTCACCTGAGGGTGCA -GCTGCTGATTACGAAGCTCGTCTGAAACAATTGATTGAGAGCAAAGTTCTTCCGTTATCA -GCAATTACTGGATTCCCCAAATTTGATCTTATGCTATTAGGTATGGGGCCAGATGGACAT -GTAGCGTCTTTGTTTCCTTTGCATCCTCACCGCCACGAGAAGGAGCGGCTGGTCACCTTC -ATTACAGACTCACCAAAACCTCCTCCACCAAGGATTACTTTCACCTTTCCGGTAATTAAT -TCGGCTTCAGAGATAGCAATGGTGGTCACAGGAGCAGAGTTAGCTCATATGGTTGATGTC -GCTTTGGGTAATGCGCCT------CCTCCTGATGGAATTCCTCCCCCTTGTACTGAGGTT -TCAGCTGAAGAGGAACTGACCTGGTTTTTAGACAAGGATGCTGCATCAGAACTA------ -------CAGACCTCTAGA ->contig_2 ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------NNCCTTTCCAAG -GTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCA -GCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCA -ACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGGCCCGACGGCCAT -GTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGGGTCACTTTC -ATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAAC -TCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATA -GCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCTTGTACTGAAGTT -TCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAACTGTTAAAT -TATGTGCGCTTTGATGAT |
| b |
| diff -r 79ea0eef1942 -r 1c5a484fc06f test-data/39614.faa.aln --- a/test-data/39614.faa.aln Tue Sep 04 08:51:38 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,36 +0,0 @@ ->gnl_Orysa6.0_PACid_16878968 -M----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------SHMEAFQNVVLLHKANSNS -TLEDISSLSAASCCSLDQLLACVEGEAQKIFGDIQNLLADHRSEVAHFTQELRESFRISL -DRTKDMSSFILGLFDKYVEETSKLQSHSNHTHEAQVKSLEDFQKAYEEQSKSEEQKLLAD -ITSLVSKHVTRQRELVGGRLNSLGDAARGNKAFLDEHTSAMEVVTKDAKRKWEMFAEQAE -NDCKVGSNFSAAKHCRMETILQECACTVDTAAQQWKASHATVNDLCRKQIAEVEALVRSA -IETNEQHEAEIASSRATAEEHASNSSKDLLQDVDNMLQEARNSSSRVVSTVEAHLGESQH -LQESHSSHTAGINTHADNAFQSSYKDYEPTGETPVRSEPEVPSKDAIESLRAMPMESLMD -EFRENHPYEPS---KDRRPSLIPRSPLATINN ->gnl_Phoda3.0_PDK_30s1023721g001 -VNQKMMKCTLIKDLYGEIERLKAEVYAAREKVGVYIPKERYHQEESERKAMAEQIEQMGV -LLENNQKQIEDLQERYNTQLQQSDDLSKKLDATEILCVSLSKKLDATEKSLEHTSKLLAA -AREDLKQAQYTLKEKDFVISEQRKAAREDKLNTANRSIVNNFRADLATRVGTLCNTVVAS -LDRQNEHLQSVEKLCQSSLDFHDKAVSELKRKVSASRALYTSHMEALQNVVRLHKASSNA -SLEEMSSMISANTCSLDQLLALGQSEADLIFSDLQSILSIHRGEIANFTRELREKFQVNL -DRTKEMSNFILELLEKIGKGTKEFQNDSTLVHEAQVKSIGDFQKAYE------------- ----------------VEVRLTGLGDAARDSKAIMDNHASSMDIVTTDAKRKWEEYSKQAE -QDSEDGSNFSAAKHCRMELMLQQCVNSVDATSQQWKKTHASVSEMSSKHVAEIEALVRSA -IESNDQHDAEVASARMAAEEDVAKNSKDVLQHFDTVIDHERNSAAGVMAAVEAHSATLHK -LQEEQSSQATEINSHAEDTFQNTYMDYEPTGETPTRSEPDIPSRGTIESLRAMPIEALLE -EFRENHPYES----KEPKPSLIPRSPLVQLN- ->contig_3 -X----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------VD------------------------EGVV--- ---------------------------------VAGLSEQEKASVSEILTTARAHSETIEN -LKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKGTIESLRAMPIDALEE -EFRENHSYESAVTGKELMPSVTTRAPFSQIN- |
| b |
| diff -r 79ea0eef1942 -r 1c5a484fc06f test-data/39614.fna.aln --- a/test-data/39614.fna.aln Tue Sep 04 08:51:38 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,99 +0,0 @@ ->gnl_Orysa6.0_PACid_16878968 -ATG--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----TCACATATGGAAGCCTTCCAAAATGTTGTGCTCCTGCATAAAGCAAATTCAAATTCT -ACACTAGAGGATATATCATCCCTATCTGCTGCAAGCTGTTGCAGCCTTGATCAGCTTCTA -GCTTGTGTCGAGGGAGAGGCACAGAAGATATTTGGTGATATCCAGAATTTGCTAGCTGAT -CATCGAAGCGAAGTGGCACATTTCACTCAAGAGTTGCGGGAGAGTTTCCGCATTAGCTTG -GATAGGACGAAGGACATGTCTAGTTTCATCCTTGGGTTGTTCGATAAGTATGTGGAGGAA -ACTTCGAAGTTGCAGAGCCACTCCAATCACACACATGAAGCACAAGTCAAAAGCCTTGAA -GATTTCCAGAAGGCTTATGAGGAGCAATCAAAATCAGAAGAACAAAAGCTTCTGGCGGAC -ATCACCAGTTTGGTTTCTAAACACGTTACTCGACAACGAGAACTGGTGGGTGGTAGACTA -AACTCTCTTGGTGACGCCGCTCGTGGAAACAAAGCATTTTTGGATGAGCACACGTCCGCC -ATGGAGGTGGTCACGAAGGACGCCAAGAGAAAGTGGGAAATGTTTGCAGAGCAGGCAGAG -AATGACTGCAAAGTTGGGTCCAACTTCTCTGCAGCTAAGCATTGTCGCATGGAAACCATT -CTGCAGGAATGTGCATGCACCGTCGACACTGCTGCTCAACAATGGAAAGCATCACATGCA -ACTGTTAACGATCTATGCAGAAAACAAATAGCTGAAGTTGAAGCACTCGTCAGGAGTGCA -ATCGAAACCAACGAGCAGCACGAAGCAGAGATTGCATCTTCCCGTGCCACGGCCGAGGAG -CATGCGTCCAACAGCAGCAAGGACCTACTCCAAGATGTTGACAATATGCTGCAGGAGGCG -CGCAATTCGTCGTCGAGAGTGGTGTCGACGGTGGAAGCTCATTTGGGAGAGAGCCAGCAT -CTACAGGAGAGCCACTCCAGCCATACCGCCGGCATCAACACCCACGCCGACAACGCTTTC -CAGAGCAGCTACAAGGACTACGAGCCGACCGGCGAAACTCCGGTGAGGTCGGAGCCGGAG -GTGCCGAGCAAAGACGCGATCGAGTCGCTGCGAGCGATGCCGATGGAGTCCCTGATGGAC -GAGTTCCGCGAGAACCACCCCTACGAGCCGAGC---------AAGGACCGCAGGCCATCG -CTCATCCCTCGCTCGCCGCTCGCCACCATCAACAAC ->gnl_Phoda3.0_PDK_30s1023721g001 -GTAAACCAAAAAATGATGAAATGTACATTAATCAAAGATCTCTATGGAGAAATTGAGCGT -CTAAAAGCAGAGGTGTATGCTGCTCGTGAGAAAGTTGGAGTTTACATACCAAAAGAACGC -TACCATCAAGAAGAGAGCGAACGGAAGGCAATGGCAGAACAAATTGAACAAATGGGGGTC -TTGCTCGAAAACAATCAAAAGCAAATTGAGGATCTACAAGAAAGGTATAATACTCAACTT -CAACAGTCTGATGACCTGAGCAAAAAGCTTGATGCCACCGAGATTCTCTGTGTTTCTCTG -AGCAAAAAGCTTGATGCCACCGAGAAAAGTTTGGAGCACACTAGCAAGTTATTGGCTGCT -GCCAGAGAAGATCTGAAGCAAGCTCAGTATACTCTGAAGGAGAAAGATTTTGTTATATCA -GAGCAGAGGAAAGCAGCTAGAGAAGACAAACTGAATACTGCCAACAGATCTATTGTGAAC -AATTTTCGGGCTGATCTTGCAACAAGGGTTGGAACACTTTGTAATACTGTTGTTGCATCC -TTGGATCGGCAAAATGAACACCTTCAGTCTGTTGAGAAACTATGTCAATCTAGCCTTGAT -TTCCATGACAAGGCAGTATCAGAGCTGAAAAGGAAAGTGTCAGCTTCAAGAGCTTTGTAT -ACTTCCCATATGGAAGCACTACAAAATGTAGTGCGTTTGCATAAGGCAAGCAGCAATGCC -AGCTTAGAAGAGATGTCATCCATGATTTCTGCCAATACCTGCTCTCTTGATCAGTTACTT -GCCTTGGGGCAAAGCGAAGCAGATCTGATTTTTAGTGATCTGCAAAGCATATTGTCAATT -CACCGAGGAGAGATTGCAAATTTCACCCGTGAACTTCGTGAGAAATTTCAAGTTAATTTG -GATCGGACAAAGGAGATGTCCAATTTTATTCTTGAGCTGCTTGAAAAGATAGGGAAGGGA -ACAAAAGAATTTCAGAATGACTCAACTTTGGTACATGAGGCTCAGGTGAAGAGCATTGGT -GATTTCCAAAAGGCATATGAG--------------------------------------- ----------------------------------------------GTGGAAGTGAGGCTC -ACTGGACTGGGAGATGCTGCTCGAGATAGCAAAGCAATTATGGATAACCATGCATCATCA -ATGGACATCGTCACAACTGATGCTAAGAGGAAGTGGGAAGAATATTCCAAGCAGGCAGAG -CAAGATTCAGAGGACGGTTCTAACTTTTCAGCAGCAAAACATTGTCGCATGGAACTCATG -CTCCAACAGTGTGTAAACTCTGTTGATGCTACTTCTCAACAGTGGAAGAAGACACATGCA -TCTGTTAGTGAGATGAGCAGCAAACACGTTGCTGAAATTGAAGCACTTGTAAGGAGTGCC -ATTGAGAGCAATGATCAGCATGATGCTGAGGTTGCTTCAGCAAGAATGGCAGCAGAAGAG -GATGTAGCGAAAAATAGCAAAGATGTTCTTCAGCATTTTGATACTGTGATTGATCATGAG -CGCAACTCAGCCGCTGGAGTGATGGCAGCAGTCGAAGCTCACTCAGCAACCCTGCATAAA -CTGCAAGAGGAACAATCAAGCCAGGCAACAGAGATTAATAGCCATGCGGAGGACACATTC -CAAAACACCTACATGGACTATGAACCAACGGGAGAAACCCCAACAAGGTCGGAACCAGAT -ATACCAAGCAGGGGAACAATCGAATCTCTTCGAGCCATGCCGATAGAAGCCCTCCTTGAA -GAGTTCCGGGAGAACCATCCATACGAGTCC------------AAGGAGCCCAAACCGTCT -CTCATACCACGCTCTCCACTCGTCCAGCTCAAC--- ->contig_3 -NNT--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------GTGGAT--------------------------------- ----------------------------------------GAAGGAGTTGTT--------- ------------------------------------------------------------- -------------------------------------GTTGCTGGCTTGTCAGAGCAGGAG -AAGGCATCTGTTTCTGAAATTCTGACAACTGCTAGAGCTCATTCAGAAACAATTGAGAAC -CTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTTTC -AGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGAT -ATTCCCAGCAAAGGCACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAA -GAATTTCGAGAAAACCATTCATACGAATCTGCTGTTACAGGAAAGGAACTAATGCCGTCT -GTTACGACTCGTGCACCATTTTCACAGATCAAC--- |
| b |
| diff -r 79ea0eef1942 -r 1c5a484fc06f utils.py --- a/utils.py Tue Sep 04 08:51:38 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,56 +0,0 @@ -import os -import shutil -import subprocess -import sys - -FSTDERR = 'stderr.txt' -FSTDOUT = 'stdout.txt' - - -def check_execution_errors(rc, fstderr, fstdout): - if rc != 0: - fh = open(fstdout, 'rb') - out_msg = fh.read() - fh.close() - fh = open(fstderr, 'rb') - err_msg = fh.read() - fh.close() - msg = '%s\n%s\n' % (str(out_msg), str(err_msg)) - stop_err(msg) - - -def get_response_buffers(): - fstderr = os.path.join(os.getcwd(), FSTDERR) - fherr = open(fstderr, 'wb') - fstdout = os.path.join(os.getcwd(), FSTDOUT) - fhout = open(fstdout, 'wb') - return fstderr, fherr, fstdout, fhout - - -def move_directory_files(source_dir, destination_dir, copy=False, remove_source_dir=False): - source_directory = os.path.abspath(source_dir) - destination_directory = os.path.abspath(destination_dir) - if not os.path.isdir(destination_directory): - os.makedirs(destination_directory) - for dir_entry in os.listdir(source_directory): - source_entry = os.path.join(source_directory, dir_entry) - if copy: - shutil.copy(source_entry, destination_directory) - else: - shutil.move(source_entry, destination_directory) - if remove_source_dir: - os.rmdir(source_directory) - - -def run_command(cmd): - fstderr, fherr, fstdout, fhout = get_response_buffers() - proc = subprocess.Popen(args=cmd, stderr=fherr, stdout=fhout, shell=True) - rc = proc.wait() - # Check results. - fherr.close() - fhout.close() - check_execution_errors(rc, fstderr, fstdout) - - -def stop_err(msg): - sys.exit(msg) |