From 1f60e9ba8fe485c3075cc1e849ab6c88bf65b313 Mon Sep 17 00:00:00 2001 From: Gonzalo Vidal <35148159+Gonza10V@users.noreply.github.com> Date: Thu, 17 Apr 2025 15:14:20 -0600 Subject: [PATCH 1/6] Delete Test directory --- Test/Part_in_backbone_defined.xml | 328 ------------------------------ Test/Part_in_backbone_example.xml | 328 ------------------------------ Test/Test_files.md | 1 - Test/ab_j23101.gb | 81 -------- Test/backbone.xml | 328 ------------------------------ Test/cds_in_bb.xml | 328 ------------------------------ Test/pro_in_bb.xml | 328 ------------------------------ Test/rbs_in_bb.xml | 328 ------------------------------ Test/terminator_in_bb.xml | 328 ------------------------------ 9 files changed, 2378 deletions(-) delete mode 100644 Test/Part_in_backbone_defined.xml delete mode 100644 Test/Part_in_backbone_example.xml delete mode 100644 Test/Test_files.md delete mode 100644 Test/ab_j23101.gb delete mode 100644 Test/backbone.xml delete mode 100644 Test/cds_in_bb.xml delete mode 100644 Test/pro_in_bb.xml delete mode 100644 Test/rbs_in_bb.xml delete mode 100644 Test/terminator_in_bb.xml diff --git a/Test/Part_in_backbone_defined.xml b/Test/Part_in_backbone_defined.xml deleted file mode 100644 index 113169b..0000000 --- a/Test/Part_in_backbone_defined.xml +++ /dev/null @@ -1,328 +0,0 @@ - - - - - module1 - - - - j0nju1Eb_56 - - - - - - - - - Cir_qKqs - 1 - Cir - - - - - - - j0nju1Eb - 1 - - - - - - - - Cir_qKqs_5 - 1 - - - - - - - - Scar_B_4 - 1 - - - - - - - - J23101_3 - 1 - - - - - - - - Scar_A_2 - 1 - - - - - - - - j0nju1EbAnnotation1 - 1 - - - - location1 - 1 - 5 - 39 - - - - - - - - - - j0nju1EbAnnotation2 - 1 - - - - location2 - 1 - 40 - 43 - - - - - - - - - - j0nju1EbAnnotation0 - 1 - - - - location0 - 1 - 1 - 4 - - - - - - - - - - j0nju1EbAnnotation3 - 1 - - - - location3 - 1 - 44 - 2095 - - - - - - - - - - j0nju1EbConstraint1 - 1 - - - - - - - - - j0nju1EbConstraint3 - 1 - - - - - - - - - j0nju1EbConstraint2 - 1 - - - - - - - - - - Scar_B - 1 - Scar_B - - - - - - - J23101 - 1 - J23101 - - - - - - - Scar_A - 1 - Scar_A - - - - - - - j0nju1Eb_sequence - GGAGtttacagctagctcagtcctaggtattatgctagcTACTCGAGaccctgcagtccggcaaaaaagggcaaggtgtcaccaccctgccctttttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccacaggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagctcgaggcttggattctcaccaataaaaaacgcccggcggcaaccgagcgttctgaacaaatccagatggagttctgaggtcattactggatctatcaacaggagtccaagcgagctcgatatcaaattacgccccgccctgccactcatcgcagtactgttgtaattcattaagcattctgccgacatggaagccatcacaaacggcatgatgaacctgaatcgccagcggcatcagcaccttgtcgccttgcgtataatatttgcccatggtgaaaacgggggcgaagaagttgtccatattggccacgtttaaatcaaaactggtgaaactcacccagggattggctgagacgaaaaacatattctcaataaaccctttagggaaataggccaggttttcaccgtaacacgccacatcttgcgaatatatgtgtagaaactgccggaaatcgtcgtggtattcactccagagcgatgaaaacgtttcagtttgctcatggaaaacggtgtaacaagggtgaacactatcccatatcaccagctcaccgtcttcattgccatacgaaattccggatgagcattcatcaggcgggcaagaatgtgaataaaggccggataaaacttgtgcttatttttctttacggtctttaaaaaggccgtaatatccagctgaacggtctggttataggtacattgagcaactgactgaaatgcctcaaaatgttctttacgatgccattgggatatatcaacggtggtatatccagtgatttttttctccattttagcttccttagctcctgaaaatctcgataactcaaaaaatacgcccggtagtgatcttatttcattatggtgaaagttggaacctcttacgtgcccgatcaactcgagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggcagaatttcagataaaaaaaatccttagctttcgctaaggatgatttctggaattcggtctcg - - - - - Cir_qKqs_sequence - CGAGaccctgcagtccggcaaaaaagggcaaggtgtcaccaccctgccctttttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccacaggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagctcgaggcttggattctcaccaataaaaaacgcccggcggcaaccgagcgttctgaacaaatccagatggagttctgaggtcattactggatctatcaacaggagtccaagcgagctcgatatcaaattacgccccgccctgccactcatcgcagtactgttgtaattcattaagcattctgccgacatggaagccatcacaaacggcatgatgaacctgaatcgccagcggcatcagcaccttgtcgccttgcgtataatatttgcccatggtgaaaacgggggcgaagaagttgtccatattggccacgtttaaatcaaaactggtgaaactcacccagggattggctgagacgaaaaacatattctcaataaaccctttagggaaataggccaggttttcaccgtaacacgccacatcttgcgaatatatgtgtagaaactgccggaaatcgtcgtggtattcactccagagcgatgaaaacgtttcagtttgctcatggaaaacggtgtaacaagggtgaacactatcccatatcaccagctcaccgtcttcattgccatacgaaattccggatgagcattcatcaggcgggcaagaatgtgaataaaggccggataaaacttgtgcttatttttctttacggtctttaaaaaggccgtaatatccagctgaacggtctggttataggtacattgagcaactgactgaaatgcctcaaaatgttctttacgatgccattgggatatatcaacggtggtatatccagtgatttttttctccattttagcttccttagctcctgaaaatctcgataactcaaaaaatacgcccggtagtgatcttatttcattatggtgaaagttggaacctcttacgtgcccgatcaactcgagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggcagaatttcagataaaaaaaatccttagctttcgctaaggatgatttctggaattcggtctcg - - - - - J23101_sequence - tttacagctagctcagtcctaggtattatgctagc - - - - - Scar_A_sequence - GGAG - - - - - Scar_B_sequence - TACT - - - - - Cir_qKqs_Layout - - - - - module1_Layout - - - - 695.0 - 457.0 - 152.0 - 100.0 - j0nju1Eb_56 - - - - - - - j0nju1Eb_Layout - - - - 695.0 - 457.0 - 152.0 - 100.0 - container - - - - - 0.0 - 50.0 - 152.0 - 1.0 - backbone - - - - - 1.0 - 0.0 - 50.0 - 100.0 - Scar_A_2 - - - - - - 51.0 - 0.0 - 50.0 - 100.0 - J23101_3 - - - - - - 101.0 - 0.0 - 50.0 - 100.0 - Scar_B_4 - - - - - - 151.0 - 0.0 - 1.0 - 100.0 - Cir_qKqs_5 - - - - - - - Scar_A_Layout - - - - - Scar_B_Layout - - - - - J23101_Layout - - - diff --git a/Test/Part_in_backbone_example.xml b/Test/Part_in_backbone_example.xml deleted file mode 100644 index 5752831..0000000 --- a/Test/Part_in_backbone_example.xml +++ /dev/null @@ -1,328 +0,0 @@ - - - - - module1 - - - - XJK9paob_2 - - - - - - - - - Scar_bWtJ - 1 - Scar - - - - - - - Scar_dAK6 - 1 - Scar - - - - - - - Pro_zVcE - 1 - Pro - - - - - - - Cir_wQ7v - 1 - Cir - - - - - - - XJK9paob - 1 - - - - - - - - Scar_dAK6_4 - 1 - - - - - - - - Pro_zVcE_3 - 1 - - - - - - - - Scar_bWtJ_2 - 1 - - - - - - - - Cir_wQ7v_5 - 1 - - - - - - - - XJK9paobAnnotation2 - 1 - - - - location2 - 1 - 12 - 15 - - - - - - - - - - XJK9paobAnnotation3 - 1 - - - - location3 - 1 - 16 - 39 - - - - - - - - - - XJK9paobAnnotation1 - 1 - - - - location1 - 1 - 5 - 11 - - - - - - - - - - XJK9paobAnnotation0 - 1 - - - - location0 - 1 - 1 - 4 - - - - - - - - - - XJK9paobConstraint1 - 1 - - - - - - - - - XJK9paobConstraint2 - 1 - - - - - - - - - XJK9paobConstraint3 - 1 - - - - - - - - - - Scar_bWtJ_sequence - AAAA - - - - - XJK9paob_sequence - AAAATTTTTTTCCCCGGGGGGGGGGGGGGGGGGGGGGGG - - - - - Pro_zVcE_sequence - TTTTTTT - - - - - Scar_dAK6_sequence - CCCC - - - - - Cir_wQ7v_sequence - GGGGGGGGGGGGGGGGGGGGGGGG - - - - - Pro_zVcE_Layout - - - - - Scar_bWtJ_Layout - - - - - module1_Layout - - - - 640.0 - 310.0 - 152.0 - 100.0 - XJK9paob_2 - - - - - - - Cir_wQ7v_Layout - - - - - Scar_dAK6_Layout - - - - - XJK9paob_Layout - - - - 640.0 - 310.0 - 152.0 - 100.0 - container - - - - - 0.0 - 50.0 - 152.0 - 1.0 - backbone - - - - - 1.0 - 0.0 - 50.0 - 100.0 - Scar_bWtJ_2 - - - - - - 51.0 - 0.0 - 50.0 - 100.0 - Pro_zVcE_3 - - - - - - 101.0 - 0.0 - 50.0 - 100.0 - Scar_dAK6_4 - - - - - - 151.0 - 0.0 - 1.0 - 100.0 - Cir_wQ7v_5 - - - - - diff --git a/Test/Test_files.md b/Test/Test_files.md deleted file mode 100644 index 7a7dae5..0000000 --- a/Test/Test_files.md +++ /dev/null @@ -1 +0,0 @@ -Test files diff --git a/Test/ab_j23101.gb b/Test/ab_j23101.gb deleted file mode 100644 index 6f534a7..0000000 --- a/Test/ab_j23101.gb +++ /dev/null @@ -1,81 +0,0 @@ -LOCUS AB_J23101 2095 bp ds-DNA circular 25-OCT-2023 -DEFINITION . -COMMENT From pSB1C00 - Loop universal L0 acceptor and J23100_B0034_AC -FEATURES Location/Qualifiers - misc_feature 346..365 - /label="VF Primer binding site" - /ApEinfo_revcolor="#b7e6d7" - /ApEinfo_fwdcolor="#b7e6d7" - misc_feature complement(422..466) - /label="Terminator" - /ApEinfo_revcolor="#c7b0e3" - /ApEinfo_fwdcolor="#c7b0e3" - BioBrick 468..473 - /label="BsaI Site" - /ApEinfo_revcolor="#f58a5e" - /ApEinfo_fwdcolor="#f58a5e" - misc_feature 475..478 - /label="A" - /ApEinfo_revcolor="#ff9ccd" - /ApEinfo_fwdcolor="#ff9ccd" - misc_feature 479..513 - /label="J23101" - /ApEinfo_revcolor="#b1ff67" - /ApEinfo_fwdcolor="#b1ff67" - misc_feature 514..517 - /label="B" - /ApEinfo_revcolor="#f8d3a9" - /ApEinfo_fwdcolor="#f8d3a9" - misc_feature 531..602 - /label="His Terminator" - /ApEinfo_revcolor="#ffef86" - /ApEinfo_fwdcolor="#ffef86" - misc_feature complement(666..685) - /label="VR Primer binding site" - /ApEinfo_revcolor="#b1ff67" - /ApEinfo_fwdcolor="#b1ff67" - misc_feature complement(770..1384) - /label="rep (pMB1)" - /ApEinfo_revcolor="#85dae9" - /ApEinfo_fwdcolor="#85dae9" - misc_feature complement(1551..1656) - /label="Terminator T0" - /ApEinfo_revcolor="#c6c9d1" - /ApEinfo_fwdcolor="#c6c9d1" -ORIGIN - 1 tcattgccat acgaaattcc ggatgagcat tcatcaggcg ggcaagaatg tgaataaagg - 61 ccggataaaa cttgtgctta tttttcttta cggtctttaa aaaggccgta atatccagct - 121 gaacggtctg gttataggta cattgagcaa ctgactgaaa tgcctcaaaa tgttctttac - 181 gatgccattg ggatatatca acggtggtat atccagtgat ttttttctcc attttagctt - 241 ccttagctcc tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat - 301 tatggtgaaa gttggaacct cttacgtgcc cgatcaactc gagtgccacc tgacgtctaa - 361 gaaaccatta ttatcatgac attaacctat aaaaataggc gtatcacgag gcagaatttc - 421 agataaaaaa aatccttagc tttcgctaag gatgatttct ggaattcggt ctcgGGAGtt - 481 tacagctagc tcagtcctag gtattatgct agcTACTCGA Gaccctgcag tccggcaaaa - 541 aagggcaagg tgtcaccacc ctgccctttt tctttaaaac cgaaaagatt acttcgcgtt - 601 atgcaggctt cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg gcgagcggta - 661 tcagctcact caaaggcggt aatacggtta tccacagaat caggggataa cgcaggaaag - 721 aacatgtgag caaaaggcca gcaaaaggcc aggaaccgta aaaaggccgc gttgctggcg - 781 tttttccaca ggctccgccc ccctgacgag catcacaaaa atcgacgctc aagtcagagg - 841 tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggaag ctccctcgtg - 901 cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct cccttcggga - 961 agcgtggcgc tttctcatag ctcacgctgt aggtatctca gttcggtgta ggtcgttcgc - 1021 tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc cttatccggt - 1081 aactatcgtc ttgagtccaa cccggtaaga cacgacttat cgccactggc agcagccact - 1141 ggtaacagga ttagcagagc gaggtatgta ggcggtgcta cagagttctt gaagtggtgg - 1201 cctaactacg gctacactag aagaacagta tttggtatct gcgctctgct gaagccagtt - 1261 accttcggaa aaagagttgg tagctcttga tccggcaaac aaaccaccgc tggtagcggt - 1321 ggtttttttg tttgcaagca gcagattacg cgcagaaaaa aaggatctca agaagatcct - 1381 ttgatctttt ctacggggtc tgacgctcag tggaacgaaa actcacgtta agggattttg - 1441 gtcatgagat tatcaaaaag gatcttcacc tagatccttt taaattaaaa atgaagtttt - 1501 aaatcaatct aaagtatata tgagtaaact tggtctgaca gctcgaggct tggattctca - 1561 ccaataaaaa acgcccggcg gcaaccgagc gttctgaaca aatccagatg gagttctgag - 1621 gtcattactg gatctatcaa caggagtcca agcgagctcg atatcaaatt acgccccgcc - 1681 ctgccactca tcgcagtact gttgtaattc attaagcatt ctgccgacat ggaagccatc - 1741 acaaacggca tgatgaacct gaatcgccag cggcatcagc accttgtcgc cttgcgtata - 1801 atatttgccc atggtgaaaa cgggggcgaa gaagttgtcc atattggcca cgtttaaatc - 1861 aaaactggtg aaactcaccc agggattggc tgagacgaaa aacatattct caataaaccc - 1921 tttagggaaa taggccaggt tttcaccgta acacgccaca tcttgcgaat atatgtgtag - 1981 aaactgccgg aaatcgtcgt ggtattcact ccagagcgat gaaaacgttt cagtttgctc - 2041 atggaaaacg gtgtaacaag ggtgaacact atcccatatc accagctcac cgtct -// \ No newline at end of file diff --git a/Test/backbone.xml b/Test/backbone.xml deleted file mode 100644 index f2a69e2..0000000 --- a/Test/backbone.xml +++ /dev/null @@ -1,328 +0,0 @@ - - - - - module1 - - - - UJHDBOTD_159 - - - - - - - - - Scar_F - 1 - Scar_F - - - - - - - RFP_cassette - 1 - RFP_cassette - - - - - - - UJHDBOTD - 1 - - - - - - - - Scar_F_4 - 1 - - - - - - - - Cir_qxow_5 - 1 - - - - - - - - Scar_A_2 - 1 - - - - - - - - RFP_cassette_3 - 1 - - - - - - - - UJHDBOTDAnnotation0 - 1 - - - - location0 - 1 - 1 - 4 - - - - - - - - - - UJHDBOTDAnnotation3 - 1 - - - - location3 - 1 - 1092 - 3286 - - - - - - - - - - UJHDBOTDAnnotation2 - 1 - - - - location2 - 1 - 1088 - 1091 - - - - - - - - - - UJHDBOTDAnnotation1 - 1 - - - - location1 - 1 - 5 - 1087 - - - - - - - - - - UJHDBOTDConstraint1 - 1 - - - - - - - - - UJHDBOTDConstraint3 - 1 - - - - - - - - - UJHDBOTDConstraint2 - 1 - - - - - - - - - - Cir_qxow - 1 - Cir - - - - - - - Scar_A - 1 - Scar_A - - - - - - - UJHDBOTD_sequence - ggagtgagacccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggcaccccaggctttacactttatgcttccggctcgtatgttgtgtggaattgtgagcggataacaatttcacacatactagagaaagaggagaaatactagatggcttcctccgaagacgttatcaaagagttcatgcgtttcaaagttcgtatggaaggttccgttaacggtcacgagttcgaaatcgaaggtgaaggtgaaggtcgtccgtacgaaggtacccagaccgctaaactgaaagttaccaaaggtggtccgctgccgttcgcttgggacatcctgtccccgcagttccagtacggttccaaagcttacgttaaacacccggctgacatcccggactacctgaaactgtccttcccggaaggtttcaaatgggaacgtgttatgaacttcgaagacggtggtgttgttaccgttacccaggactcctccctgcaagacggtgagttcatctacaaagttaaactgcgtggtaccaacttcccgtccgacggtccggttatgcagaaaaaaaccatgggttgggaagcttccaccgaacgtatgtacccggaagacggtgctctgaaaggtgaaatcaaaatgcgtctgaaactgaaagacggtggtcactacgacgctgaagttaaaaccacctacatggctaaaaaaccggttcagctgccgggtgcttacaaaaccgacatcaaactggacatcacctcccacaacgaagactacaccatcgttgaacagtacgaacgtgctgaaggtcgtcactccaccggtgcttaataacgctgatagtgctagtgtagatcgctactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttataggtctcacgctgcatgaagagcctgcagtccggcaaaaaagggcaaggtgtcaccaccctgccctttttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccacaggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagctcgagtcccgtcaagtcagcgtaatgctctgccagtgttacaaccaattaaccaattctgattagaaaaactcatcgagcatcaaatgaaactgcaatttattcatatcaggattatcaataccatatttttgaaaaagccgtttctgtaatgaaggagaaaactcaccgaggcagttccataggatggcaagatcctggtatcggtctgcgattccgactcgtccaacatcaatacaacctattaatttcccctcgtcaaaaataaggttatcaagtgagaaatcaccatgagtgacgactgaatccggtgagaatggcaaaagcttatgcatttctttccagacttgttcaacaggccagccattacgctcgtcatcaaaatcactcgcatcaaccaaaccgttattcattcgtgattgcgcctgagcgagacgaaatacgcgatcgctgttaaaaggacaattacaaacaggaatcgaatgcaaccggcgcaggaacactgccagcgcatcaacaatattttcacctgaatcaggatattcttctaatacctggaatgctgttttcccggggatcgcagtggtgagtaaccatgcatcatcaggagtacggataaaatgcttgatggtcggaagaggcataaattccgtcagccagtttagtctgaccatctcatctgtaacatcattggcaacgctacctttgccatgtttcagaaacaactctggcgcatcgggcttcccatacaatcgatagattgtcgcacctgattgcccgacattatcgcgagcccatttatacccatataaatcagcatccatgttggaatttaatcgcggcctggagcaagacgtttcccgttgaatatggctcataacaccccttgtattactgtttatgtaagcagacagttttattgttcatgatgatatatttttatcttgtgcaatgtaacatcagagattttgagacacaacgtggctttgttgaataaatcgaacttttgctgagttgaaggatcagctcgagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggcagaatttcagataaaaaaaatccttagctttcgctaaggatgatttctggaattcgctcttcaatg - - - - - Scar_F_sequence - cgct - - - - - Cir_qxow_sequence - gcatgaagagcctgcagtccggcaaaaaagggcaaggtgtcaccaccctgccctttttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccacaggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagctcgagtcccgtcaagtcagcgtaatgctctgccagtgttacaaccaattaaccaattctgattagaaaaactcatcgagcatcaaatgaaactgcaatttattcatatcaggattatcaataccatatttttgaaaaagccgtttctgtaatgaaggagaaaactcaccgaggcagttccataggatggcaagatcctggtatcggtctgcgattccgactcgtccaacatcaatacaacctattaatttcccctcgtcaaaaataaggttatcaagtgagaaatcaccatgagtgacgactgaatccggtgagaatggcaaaagcttatgcatttctttccagacttgttcaacaggccagccattacgctcgtcatcaaaatcactcgcatcaaccaaaccgttattcattcgtgattgcgcctgagcgagacgaaatacgcgatcgctgttaaaaggacaattacaaacaggaatcgaatgcaaccggcgcaggaacactgccagcgcatcaacaatattttcacctgaatcaggatattcttctaatacctggaatgctgttttcccggggatcgcagtggtgagtaaccatgcatcatcaggagtacggataaaatgcttgatggtcggaagaggcataaattccgtcagccagtttagtctgaccatctcatctgtaacatcattggcaacgctacctttgccatgtttcagaaacaactctggcgcatcgggcttcccatacaatcgatagattgtcgcacctgattgcccgacattatcgcgagcccatttatacccatataaatcagcatccatgttggaatttaatcgcggcctggagcaagacgtttcccgttgaatatggctcataacaccccttgtattactgtttatgtaagcagacagttttattgttcatgatgatatatttttatcttgtgcaatgtaacatcagagattttgagacacaacgtggctttgttgaataaatcgaacttttgctgagttgaaggatcagctcgagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggcagaatttcagataaaaaaaatccttagctttcgctaaggatgatttctggaattcgctcttcaatg - - - - - RFP_cassette_sequence - tgagacccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggcaccccaggctttacactttatgcttccggctcgtatgttgtgtggaattgtgagcggataacaatttcacacatactagagaaagaggagaaatactagatggcttcctccgaagacgttatcaaagagttcatgcgtttcaaagttcgtatggaaggttccgttaacggtcacgagttcgaaatcgaaggtgaaggtgaaggtcgtccgtacgaaggtacccagaccgctaaactgaaagttaccaaaggtggtccgctgccgttcgcttgggacatcctgtccccgcagttccagtacggttccaaagcttacgttaaacacccggctgacatcccggactacctgaaactgtccttcccggaaggtttcaaatgggaacgtgttatgaacttcgaagacggtggtgttgttaccgttacccaggactcctccctgcaagacggtgagttcatctacaaagttaaactgcgtggtaccaacttcccgtccgacggtccggttatgcagaaaaaaaccatgggttgggaagcttccaccgaacgtatgtacccggaagacggtgctctgaaaggtgaaatcaaaatgcgtctgaaactgaaagacggtggtcactacgacgctgaagttaaaaccacctacatggctaaaaaaccggttcagctgccgggtgcttacaaaaccgacatcaaactggacatcacctcccacaacgaagactacaccatcgttgaacagtacgaacgtgctgaaggtcgtcactccaccggtgcttaataacgctgatagtgctagtgtagatcgctactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttataggtctca - - - - - Scar_A_sequence - ggag - - - - - Cir_qxow_Layout - - - - - Scar_A_Layout - - - - - UJHDBOTD_Layout - - - - 695.0 - 457.0 - 152.0 - 100.0 - container - - - - - 0.0 - 50.0 - 152.0 - 1.0 - backbone - - - - - 1.0 - 0.0 - 50.0 - 100.0 - Scar_A_2 - - - - - - 51.0 - 0.0 - 50.0 - 100.0 - RFP_cassette_3 - - - - - - 101.0 - 0.0 - 50.0 - 100.0 - Scar_F_4 - - - - - - 151.0 - 0.0 - 1.0 - 100.0 - Cir_qxow_5 - - - - - - - Scar_F_Layout - - - - - RFP_cassette_Layout - - - - - module1_Layout - - - - 695.0 - 457.0 - 152.0 - 100.0 - UJHDBOTD_159 - - - - - diff --git a/Test/cds_in_bb.xml b/Test/cds_in_bb.xml deleted file mode 100644 index 54eb11d..0000000 --- a/Test/cds_in_bb.xml +++ /dev/null @@ -1,328 +0,0 @@ - - - - - module1 - - - - UJHDBOTD_106 - - - - - - - - - GFP - 1 - GFP - - - - - - - Scar_C - 1 - Scar_C - - - - - - - Scar_D - 1 - Scar_D - - - - - - - Cir_qxow - 1 - Cir - - - - - - - UJHDBOTD - 1 - - - - - - - - Scar_D_4 - 1 - - - - - - - - GFP_3 - 1 - - - - - - - - Cir_qxow_5 - 1 - - - - - - - - Scar_C_2 - 1 - - - - - - - - UJHDBOTDAnnotation0 - 1 - - - - location0 - 1 - 1 - 4 - - - - - - - - - - UJHDBOTDAnnotation2 - 1 - - - - location2 - 1 - 722 - 725 - - - - - - - - - - UJHDBOTDAnnotation1 - 1 - - - - location1 - 1 - 5 - 721 - - - - - - - - - - UJHDBOTDAnnotation3 - 1 - - - - location3 - 1 - 726 - 2777 - - - - - - - - - - UJHDBOTDConstraint3 - 1 - - - - - - - - - UJHDBOTDConstraint2 - 1 - - - - - - - - - UJHDBOTDConstraint1 - 1 - - - - - - - - - - Scar_C_sequence - aatg - - - - - GFP_sequence - gtgagcaagggcgaggagctgttcaccggggtggtgcccatcctggtcgagctggacggcgacgtaaacggccacaagttcagcgtgtccggcgagggcgagggcgatgccacctacggcaagctgaccctgaagttcatctgcaccaccggcaagctgcccgtgccctggcccaccctcgtgaccaccttcagctacggcgtgcagtgcttcagccgctaccccgaccacatgaagcagcacgacttcttcaagtccgccatgcccgaaggctacgtccaggagcgcaccatcttcttcaaggacgacggcaactacaagacccgcgccgaggtgaagttcgagggcgacaccctggtgaaccgcatcgagctgaagggcatcgacttcaaggaggacggcaacatcctggggcacaagctggagtacaactacaacagccacaacgtctatatcatggccgacaagcagaagaacggcatcaaggtgaacttcaagatccgccacaacatcgaggacggcagcgtgcagctcgccgaccactaccagcagaacacccccatcggcgacggccccgtgctgctgcccgacaaccactacctgagcacccagtccgccctgagcaaagaccccaacgagaagcgcgatcacatggtcctgctggagttcgtgaccgccgccgggatcactcacggcatggacgagctgtacaagtaa - - - - - Scar_D_sequence - gctt - - - - - UJHDBOTD_sequence - aatggtgagcaagggcgaggagctgttcaccggggtggtgcccatcctggtcgagctggacggcgacgtaaacggccacaagttcagcgtgtccggcgagggcgagggcgatgccacctacggcaagctgaccctgaagttcatctgcaccaccggcaagctgcccgtgccctggcccaccctcgtgaccaccttcagctacggcgtgcagtgcttcagccgctaccccgaccacatgaagcagcacgacttcttcaagtccgccatgcccgaaggctacgtccaggagcgcaccatcttcttcaaggacgacggcaactacaagacccgcgccgaggtgaagttcgagggcgacaccctggtgaaccgcatcgagctgaagggcatcgacttcaaggaggacggcaacatcctggggcacaagctggagtacaactacaacagccacaacgtctatatcatggccgacaagcagaagaacggcatcaaggtgaacttcaagatccgccacaacatcgaggacggcagcgtgcagctcgccgaccactaccagcagaacacccccatcggcgacggccccgtgctgctgcccgacaaccactacctgagcacccagtccgccctgagcaaagaccccaacgagaagcgcgatcacatggtcctgctggagttcgtgaccgccgccgggatcactcacggcatggacgagctgtacaagtaagcttCGAGaccctgcagtccggcaaaaaagggcaaggtgtcaccaccctgccctttttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccacaggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagctcgaggcttggattctcaccaataaaaaacgcccggcggcaaccgagcgttctgaacaaatccagatggagttctgaggtcattactggatctatcaacaggagtccaagcgagctcgatatcaaattacgccccgccctgccactcatcgcagtactgttgtaattcattaagcattctgccgacatggaagccatcacaaacggcatgatgaacctgaatcgccagcggcatcagcaccttgtcgccttgcgtataatatttgcccatggtgaaaacgggggcgaagaagttgtccatattggccacgtttaaatcaaaactggtgaaactcacccagggattggctgagacgaaaaacatattctcaataaaccctttagggaaataggccaggttttcaccgtaacacgccacatcttgcgaatatatgtgtagaaactgccggaaatcgtcgtggtattcactccagagcgatgaaaacgtttcagtttgctcatggaaaacggtgtaacaagggtgaacactatcccatatcaccagctcaccgtcttcattgccatacgaaattccggatgagcattcatcaggcgggcaagaatgtgaataaaggccggataaaacttgtgcttatttttctttacggtctttaaaaaggccgtaatatccagctgaacggtctggttataggtacattgagcaactgactgaaatgcctcaaaatgttctttacgatgccattgggatatatcaacggtggtatatccagtgatttttttctccattttagcttccttagctcctgaaaatctcgataactcaaaaaatacgcccggtagtgatcttatttcattatggtgaaagttggaacctcttacgtgcccgatcaactcgagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggcagaatttcagataaaaaaaatccttagctttcgctaaggatgatttctggaattcggtctcg - - - - - Cir_qxow_sequence - CGAGaccctgcagtccggcaaaaaagggcaaggtgtcaccaccctgccctttttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccacaggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagctcgaggcttggattctcaccaataaaaaacgcccggcggcaaccgagcgttctgaacaaatccagatggagttctgaggtcattactggatctatcaacaggagtccaagcgagctcgatatcaaattacgccccgccctgccactcatcgcagtactgttgtaattcattaagcattctgccgacatggaagccatcacaaacggcatgatgaacctgaatcgccagcggcatcagcaccttgtcgccttgcgtataatatttgcccatggtgaaaacgggggcgaagaagttgtccatattggccacgtttaaatcaaaactggtgaaactcacccagggattggctgagacgaaaaacatattctcaataaaccctttagggaaataggccaggttttcaccgtaacacgccacatcttgcgaatatatgtgtagaaactgccggaaatcgtcgtggtattcactccagagcgatgaaaacgtttcagtttgctcatggaaaacggtgtaacaagggtgaacactatcccatatcaccagctcaccgtcttcattgccatacgaaattccggatgagcattcatcaggcgggcaagaatgtgaataaaggccggataaaacttgtgcttatttttctttacggtctttaaaaaggccgtaatatccagctgaacggtctggttataggtacattgagcaactgactgaaatgcctcaaaatgttctttacgatgccattgggatatatcaacggtggtatatccagtgatttttttctccattttagcttccttagctcctgaaaatctcgataactcaaaaaatacgcccggtagtgatcttatttcattatggtgaaagttggaacctcttacgtgcccgatcaactcgagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggcagaatttcagataaaaaaaatccttagctttcgctaaggatgatttctggaattcggtctcg - - - - - UJHDBOTD_Layout - - - - 695.0 - 457.0 - 152.0 - 100.0 - container - - - - - 0.0 - 50.0 - 152.0 - 1.0 - backbone - - - - - 1.0 - 0.0 - 50.0 - 100.0 - Scar_C_2 - - - - - - 51.0 - 0.0 - 50.0 - 100.0 - GFP_3 - - - - - - 101.0 - 0.0 - 50.0 - 100.0 - Scar_D_4 - - - - - - 151.0 - 0.0 - 1.0 - 100.0 - Cir_qxow_5 - - - - - - - module1_Layout - - - - 695.0 - 457.0 - 152.0 - 100.0 - UJHDBOTD_106 - - - - - - - GFP_Layout - - - - - Cir_qxow_Layout - - - - - Scar_D_Layout - - - - - Scar_C_Layout - - - diff --git a/Test/pro_in_bb.xml b/Test/pro_in_bb.xml deleted file mode 100644 index 773ce8d..0000000 --- a/Test/pro_in_bb.xml +++ /dev/null @@ -1,328 +0,0 @@ - - - - - module1 - - - - UJHDBOTD_70 - - - - - - - - - Scar_B - 1 - Scar_B - - - - - - - UJHDBOTD - 1 - - - - - - - - J23101_3 - 1 - - - - - - - - Cir_qxow_5 - 1 - - - - - - - - Scar_B_4 - 1 - - - - - - - - Scar_A_2 - 1 - - - - - - - - UJHDBOTDAnnotation0 - 1 - - - - location0 - 1 - 1 - 4 - - - - - - - - - - UJHDBOTDAnnotation1 - 1 - - - - location1 - 1 - 5 - 39 - - - - - - - - - - UJHDBOTDAnnotation3 - 1 - - - - location3 - 1 - 44 - 2095 - - - - - - - - - - UJHDBOTDAnnotation2 - 1 - - - - location2 - 1 - 40 - 43 - - - - - - - - - - UJHDBOTDConstraint3 - 1 - - - - - - - - - UJHDBOTDConstraint2 - 1 - - - - - - - - - UJHDBOTDConstraint1 - 1 - - - - - - - - - - J23101 - 1 - J23101 - - - - - - - Cir_qxow - 1 - Cir - - - - - - - Scar_A - 1 - Scar_A - - - - - - - UJHDBOTD_sequence - GGAGtttacagctagctcagtcctaggtattatgctagcTACTCGAGaccctgcagtccggcaaaaaagggcaaggtgtcaccaccctgccctttttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccacaggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagctcgaggcttggattctcaccaataaaaaacgcccggcggcaaccgagcgttctgaacaaatccagatggagttctgaggtcattactggatctatcaacaggagtccaagcgagctcgatatcaaattacgccccgccctgccactcatcgcagtactgttgtaattcattaagcattctgccgacatggaagccatcacaaacggcatgatgaacctgaatcgccagcggcatcagcaccttgtcgccttgcgtataatatttgcccatggtgaaaacgggggcgaagaagttgtccatattggccacgtttaaatcaaaactggtgaaactcacccagggattggctgagacgaaaaacatattctcaataaaccctttagggaaataggccaggttttcaccgtaacacgccacatcttgcgaatatatgtgtagaaactgccggaaatcgtcgtggtattcactccagagcgatgaaaacgtttcagtttgctcatggaaaacggtgtaacaagggtgaacactatcccatatcaccagctcaccgtcttcattgccatacgaaattccggatgagcattcatcaggcgggcaagaatgtgaataaaggccggataaaacttgtgcttatttttctttacggtctttaaaaaggccgtaatatccagctgaacggtctggttataggtacattgagcaactgactgaaatgcctcaaaatgttctttacgatgccattgggatatatcaacggtggtatatccagtgatttttttctccattttagcttccttagctcctgaaaatctcgataactcaaaaaatacgcccggtagtgatcttatttcattatggtgaaagttggaacctcttacgtgcccgatcaactcgagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggcagaatttcagataaaaaaaatccttagctttcgctaaggatgatttctggaattcggtctcg - - - - - J23101_sequence - tttacagctagctcagtcctaggtattatgctagc - - - - - Cir_qxow_sequence - CGAGaccctgcagtccggcaaaaaagggcaaggtgtcaccaccctgccctttttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccacaggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagctcgaggcttggattctcaccaataaaaaacgcccggcggcaaccgagcgttctgaacaaatccagatggagttctgaggtcattactggatctatcaacaggagtccaagcgagctcgatatcaaattacgccccgccctgccactcatcgcagtactgttgtaattcattaagcattctgccgacatggaagccatcacaaacggcatgatgaacctgaatcgccagcggcatcagcaccttgtcgccttgcgtataatatttgcccatggtgaaaacgggggcgaagaagttgtccatattggccacgtttaaatcaaaactggtgaaactcacccagggattggctgagacgaaaaacatattctcaataaaccctttagggaaataggccaggttttcaccgtaacacgccacatcttgcgaatatatgtgtagaaactgccggaaatcgtcgtggtattcactccagagcgatgaaaacgtttcagtttgctcatggaaaacggtgtaacaagggtgaacactatcccatatcaccagctcaccgtcttcattgccatacgaaattccggatgagcattcatcaggcgggcaagaatgtgaataaaggccggataaaacttgtgcttatttttctttacggtctttaaaaaggccgtaatatccagctgaacggtctggttataggtacattgagcaactgactgaaatgcctcaaaatgttctttacgatgccattgggatatatcaacggtggtatatccagtgatttttttctccattttagcttccttagctcctgaaaatctcgataactcaaaaaatacgcccggtagtgatcttatttcattatggtgaaagttggaacctcttacgtgcccgatcaactcgagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggcagaatttcagataaaaaaaatccttagctttcgctaaggatgatttctggaattcggtctcg - - - - - Scar_A_sequence - GGAG - - - - - Scar_B_sequence - TACT - - - - - module1_Layout - - - - 695.0 - 457.0 - 152.0 - 100.0 - UJHDBOTD_70 - - - - - - - Cir_qxow_Layout - - - - - Scar_A_Layout - - - - - UJHDBOTD_Layout - - - - 695.0 - 457.0 - 152.0 - 100.0 - container - - - - - 0.0 - 50.0 - 152.0 - 1.0 - backbone - - - - - 1.0 - 0.0 - 50.0 - 100.0 - Scar_A_2 - - - - - - 51.0 - 0.0 - 50.0 - 100.0 - J23101_3 - - - - - - 101.0 - 0.0 - 50.0 - 100.0 - Scar_B_4 - - - - - - 151.0 - 0.0 - 1.0 - 100.0 - Cir_qxow_5 - - - - - - - Scar_B_Layout - - - - - J23101_Layout - - - diff --git a/Test/rbs_in_bb.xml b/Test/rbs_in_bb.xml deleted file mode 100644 index a1ddebd..0000000 --- a/Test/rbs_in_bb.xml +++ /dev/null @@ -1,328 +0,0 @@ - - - - - module1 - - - - UJHDBOTD_45 - - - - - - - - - UJHDBOTD - 1 - - - - - - - - Scar_B_2 - 1 - - - - - - - - B0034_3 - 1 - - - - - - - - Cir_qxow_5 - 1 - - - - - - - - Scar_C_4 - 1 - - - - - - - - UJHDBOTDAnnotation3 - 1 - - - - location3 - 1 - 30 - 2081 - - - - - - - - - - UJHDBOTDAnnotation0 - 1 - - - - location0 - 1 - 1 - 4 - - - - - - - - - - UJHDBOTDAnnotation2 - 1 - - - - location2 - 1 - 26 - 29 - - - - - - - - - - UJHDBOTDAnnotation1 - 1 - - - - location1 - 1 - 5 - 25 - - - - - - - - - - UJHDBOTDConstraint3 - 1 - - - - - - - - - UJHDBOTDConstraint1 - 1 - - - - - - - - - UJHDBOTDConstraint2 - 1 - - - - - - - - - - Scar_B - 1 - Scar_B - - - - - - - Scar_C - 1 - Scar_C - - - - - - - B0034 - 1 - B0034 - - - - - - - Cir_qxow - 1 - Cir - - - - - - - Scar_C_sequence - aatg - - - - - B0034_sequence - agagaaagaggagaaatacta - - - - - Cir_qxow_sequence - CGAGaccctgcagtccggcaaaaaagggcaaggtgtcaccaccctgccctttttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccacaggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagctcgaggcttggattctcaccaataaaaaacgcccggcggcaaccgagcgttctgaacaaatccagatggagttctgaggtcattactggatctatcaacaggagtccaagcgagctcgatatcaaattacgccccgccctgccactcatcgcagtactgttgtaattcattaagcattctgccgacatggaagccatcacaaacggcatgatgaacctgaatcgccagcggcatcagcaccttgtcgccttgcgtataatatttgcccatggtgaaaacgggggcgaagaagttgtccatattggccacgtttaaatcaaaactggtgaaactcacccagggattggctgagacgaaaaacatattctcaataaaccctttagggaaataggccaggttttcaccgtaacacgccacatcttgcgaatatatgtgtagaaactgccggaaatcgtcgtggtattcactccagagcgatgaaaacgtttcagtttgctcatggaaaacggtgtaacaagggtgaacactatcccatatcaccagctcaccgtcttcattgccatacgaaattccggatgagcattcatcaggcgggcaagaatgtgaataaaggccggataaaacttgtgcttatttttctttacggtctttaaaaaggccgtaatatccagctgaacggtctggttataggtacattgagcaactgactgaaatgcctcaaaatgttctttacgatgccattgggatatatcaacggtggtatatccagtgatttttttctccattttagcttccttagctcctgaaaatctcgataactcaaaaaatacgcccggtagtgatcttatttcattatggtgaaagttggaacctcttacgtgcccgatcaactcgagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggcagaatttcagataaaaaaaatccttagctttcgctaaggatgatttctggaattcggtctcg - - - - - UJHDBOTD_sequence - TACTagagaaagaggagaaatactaaatgCGAGaccctgcagtccggcaaaaaagggcaaggtgtcaccaccctgccctttttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccacaggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagctcgaggcttggattctcaccaataaaaaacgcccggcggcaaccgagcgttctgaacaaatccagatggagttctgaggtcattactggatctatcaacaggagtccaagcgagctcgatatcaaattacgccccgccctgccactcatcgcagtactgttgtaattcattaagcattctgccgacatggaagccatcacaaacggcatgatgaacctgaatcgccagcggcatcagcaccttgtcgccttgcgtataatatttgcccatggtgaaaacgggggcgaagaagttgtccatattggccacgtttaaatcaaaactggtgaaactcacccagggattggctgagacgaaaaacatattctcaataaaccctttagggaaataggccaggttttcaccgtaacacgccacatcttgcgaatatatgtgtagaaactgccggaaatcgtcgtggtattcactccagagcgatgaaaacgtttcagtttgctcatggaaaacggtgtaacaagggtgaacactatcccatatcaccagctcaccgtcttcattgccatacgaaattccggatgagcattcatcaggcgggcaagaatgtgaataaaggccggataaaacttgtgcttatttttctttacggtctttaaaaaggccgtaatatccagctgaacggtctggttataggtacattgagcaactgactgaaatgcctcaaaatgttctttacgatgccattgggatatatcaacggtggtatatccagtgatttttttctccattttagcttccttagctcctgaaaatctcgataactcaaaaaatacgcccggtagtgatcttatttcattatggtgaaagttggaacctcttacgtgcccgatcaactcgagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggcagaatttcagataaaaaaaatccttagctttcgctaaggatgatttctggaattcggtctcg - - - - - Scar_B_sequence - TACT - - - - - module1_Layout - - - - 695.0 - 457.0 - 152.0 - 100.0 - UJHDBOTD_45 - - - - - - - B0034_Layout - - - - - UJHDBOTD_Layout - - - - 695.0 - 457.0 - 152.0 - 100.0 - container - - - - - 0.0 - 50.0 - 152.0 - 1.0 - backbone - - - - - 1.0 - 0.0 - 50.0 - 100.0 - Scar_B_2 - - - - - - 51.0 - 0.0 - 50.0 - 100.0 - B0034_3 - - - - - - 101.0 - 0.0 - 50.0 - 100.0 - Scar_C_4 - - - - - - 151.0 - 0.0 - 1.0 - 100.0 - Cir_qxow_5 - - - - - - - Cir_qxow_Layout - - - - - Scar_B_Layout - - - - - Scar_C_Layout - - - diff --git a/Test/terminator_in_bb.xml b/Test/terminator_in_bb.xml deleted file mode 100644 index 704245a..0000000 --- a/Test/terminator_in_bb.xml +++ /dev/null @@ -1,328 +0,0 @@ - - - - - module1 - - - - UJHDBOTD_134 - - - - - - - - - B0015 - 1 - B0015 - - - - - - - Scar_F - 1 - Scar_F - - - - - - - UJHDBOTD - 1 - - - - - - - - B0015_3 - 1 - - - - - - - - Scar_F_4 - 1 - - - - - - - - Scar_D_2 - 1 - - - - - - - - Cir_qxow_5 - 1 - - - - - - - - UJHDBOTDAnnotation2 - 1 - - - - location2 - 1 - 134 - 137 - - - - - - - - - - UJHDBOTDAnnotation1 - 1 - - - - location1 - 1 - 5 - 133 - - - - - - - - - - UJHDBOTDAnnotation0 - 1 - - - - location0 - 1 - 1 - 4 - - - - - - - - - - UJHDBOTDAnnotation3 - 1 - - - - location3 - 1 - 138 - 2189 - - - - - - - - - - UJHDBOTDConstraint2 - 1 - - - - - - - - - UJHDBOTDConstraint3 - 1 - - - - - - - - - UJHDBOTDConstraint1 - 1 - - - - - - - - - - Scar_D - 1 - Scar_D - - - - - - - Cir_qxow - 1 - Cir - - - - - - - Scar_F_sequence - cgct - - - - - Scar_D_sequence - gctt - - - - - B0015_sequence - ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata - - - - - Cir_qxow_sequence - CGAGaccctgcagtccggcaaaaaagggcaaggtgtcaccaccctgccctttttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccacaggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagctcgaggcttggattctcaccaataaaaaacgcccggcggcaaccgagcgttctgaacaaatccagatggagttctgaggtcattactggatctatcaacaggagtccaagcgagctcgatatcaaattacgccccgccctgccactcatcgcagtactgttgtaattcattaagcattctgccgacatggaagccatcacaaacggcatgatgaacctgaatcgccagcggcatcagcaccttgtcgccttgcgtataatatttgcccatggtgaaaacgggggcgaagaagttgtccatattggccacgtttaaatcaaaactggtgaaactcacccagggattggctgagacgaaaaacatattctcaataaaccctttagggaaataggccaggttttcaccgtaacacgccacatcttgcgaatatatgtgtagaaactgccggaaatcgtcgtggtattcactccagagcgatgaaaacgtttcagtttgctcatggaaaacggtgtaacaagggtgaacactatcccatatcaccagctcaccgtcttcattgccatacgaaattccggatgagcattcatcaggcgggcaagaatgtgaataaaggccggataaaacttgtgcttatttttctttacggtctttaaaaaggccgtaatatccagctgaacggtctggttataggtacattgagcaactgactgaaatgcctcaaaatgttctttacgatgccattgggatatatcaacggtggtatatccagtgatttttttctccattttagcttccttagctcctgaaaatctcgataactcaaaaaatacgcccggtagtgatcttatttcattatggtgaaagttggaacctcttacgtgcccgatcaactcgagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggcagaatttcagataaaaaaaatccttagctttcgctaaggatgatttctggaattcggtctcg - - - - - UJHDBOTD_sequence - gcttccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttatacgctCGAGaccctgcagtccggcaaaaaagggcaaggtgtcaccaccctgccctttttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccacaggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagctcgaggcttggattctcaccaataaaaaacgcccggcggcaaccgagcgttctgaacaaatccagatggagttctgaggtcattactggatctatcaacaggagtccaagcgagctcgatatcaaattacgccccgccctgccactcatcgcagtactgttgtaattcattaagcattctgccgacatggaagccatcacaaacggcatgatgaacctgaatcgccagcggcatcagcaccttgtcgccttgcgtataatatttgcccatggtgaaaacgggggcgaagaagttgtccatattggccacgtttaaatcaaaactggtgaaactcacccagggattggctgagacgaaaaacatattctcaataaaccctttagggaaataggccaggttttcaccgtaacacgccacatcttgcgaatatatgtgtagaaactgccggaaatcgtcgtggtattcactccagagcgatgaaaacgtttcagtttgctcatggaaaacggtgtaacaagggtgaacactatcccatatcaccagctcaccgtcttcattgccatacgaaattccggatgagcattcatcaggcgggcaagaatgtgaataaaggccggataaaacttgtgcttatttttctttacggtctttaaaaaggccgtaatatccagctgaacggtctggttataggtacattgagcaactgactgaaatgcctcaaaatgttctttacgatgccattgggatatatcaacggtggtatatccagtgatttttttctccattttagcttccttagctcctgaaaatctcgataactcaaaaaatacgcccggtagtgatcttatttcattatggtgaaagttggaacctcttacgtgcccgatcaactcgagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggcagaatttcagataaaaaaaatccttagctttcgctaaggatgatttctggaattcggtctcg - - - - - B0015_Layout - - - - - Cir_qxow_Layout - - - - - module1_Layout - - - - 695.0 - 457.0 - 152.0 - 100.0 - UJHDBOTD_134 - - - - - - - UJHDBOTD_Layout - - - - 695.0 - 457.0 - 152.0 - 100.0 - container - - - - - 0.0 - 50.0 - 152.0 - 1.0 - backbone - - - - - 1.0 - 0.0 - 50.0 - 100.0 - Scar_D_2 - - - - - - 51.0 - 0.0 - 50.0 - 100.0 - B0015_3 - - - - - - 101.0 - 0.0 - 50.0 - 100.0 - Scar_F_4 - - - - - - 151.0 - 0.0 - 1.0 - 100.0 - Cir_qxow_5 - - - - - - - Scar_D_Layout - - - - - Scar_F_Layout - - - From 48be558cb63936350bd5fc5d20ba6efb9e968342 Mon Sep 17 00:00:00 2001 From: Gonzalo Vidal <35148159+Gonza10V@users.noreply.github.com> Date: Thu, 17 Apr 2025 15:14:37 -0600 Subject: [PATCH 2/6] Delete digestion2_test.xml --- digestion2_test.xml | 443 -------------------------------------------- 1 file changed, 443 deletions(-) delete mode 100644 digestion2_test.xml diff --git a/digestion2_test.xml b/digestion2_test.xml deleted file mode 100644 index 75d31fc..0000000 --- a/digestion2_test.xml +++ /dev/null @@ -1,443 +0,0 @@ - - - - - - - - - j0nju1Eb_56 - - - module1 - - - - - - 1 - - - - - reaction_component - - - new_assembly_plan - - - - - - 1 - - product_component - - - - - - - - - - 1 - restriction - - - - asssembly_plan_interaction - 1 - - - - - product_participation - 1 - - - - - - reactant_participation - 1 - - - - - - - - - - 1 - - - - - reactant_component - 1 - - - - - - - - BsaI_enzyme - - 1 - - - - - - - - Cir_qKqs - - - - Cir - 1 - - - - - 1 - Scar_A_2 - - - - - - - - j0nju1EbAnnotation0 - - 1 - - - - location0 - 4 - 1 - - - 1 - - - - - - - - 1 - J23101_3 - - - - - - - 1 - - j0nju1EbConstraint3 - - - - - - - - 1 - j0nju1EbAnnotation1 - - - - 1 - - - 5 - 39 - location1 - - - - - - - - 1 - - j0nju1EbConstraint1 - - - - - - - - - 1 - Cir_qKqs_5 - - - - - - - - Scar_B_4 - - - 1 - - - - 1 - - - - - j0nju1EbAnnotation2 - - - 1 - - 43 - location2 - - 40 - - - 1 - - - - - - - - - - - - - - j0nju1EbConstraint2 - 1 - - - - - - j0nju1EbAnnotation3 - - - 1 - - location3 - 2095 - - 44 - - - 1 - - - - j0nju1Eb - - - Scar_B - - Scar_B - - - - 1 - - - J23101 - - J23101 - - - 1 - - - - Scar_A - - - - Scar_A - - 1 - - - - - 1 - j0nju1Eb_part_extract - - - - fusion_sites_annotation - - - - 1 - - 43 - three_prime_fusion_site_location - 40 - - - - 1 - - - 1 - - - 4 - five_prime_fusion_site_location - 1 - - - - - - - - - - j0nju1Eb_sequence - GGAGtttacagctagctcagtcctaggtattatgctagcTACTCGAGaccctgcagtccggcaaaaaagggcaaggtgtcaccaccctgccctttttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccacaggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagctcgaggcttggattctcaccaataaaaaacgcccggcggcaaccgagcgttctgaacaaatccagatggagttctgaggtcattactggatctatcaacaggagtccaagcgagctcgatatcaaattacgccccgccctgccactcatcgcagtactgttgtaattcattaagcattctgccgacatggaagccatcacaaacggcatgatgaacctgaatcgccagcggcatcagcaccttgtcgccttgcgtataatatttgcccatggtgaaaacgggggcgaagaagttgtccatattggccacgtttaaatcaaaactggtgaaactcacccagggattggctgagacgaaaaacatattctcaataaaccctttagggaaataggccaggttttcaccgtaacacgccacatcttgcgaatatatgtgtagaaactgccggaaatcgtcgtggtattcactccagagcgatgaaaacgtttcagtttgctcatggaaaacggtgtaacaagggtgaacactatcccatatcaccagctcaccgtcttcattgccatacgaaattccggatgagcattcatcaggcgggcaagaatgtgaataaaggccggataaaacttgtgcttatttttctttacggtctttaaaaaggccgtaatatccagctgaacggtctggttataggtacattgagcaactgactgaaatgcctcaaaatgttctttacgatgccattgggatatatcaacggtggtatatccagtgatttttttctccattttagcttccttagctcctgaaaatctcgataactcaaaaaatacgcccggtagtgatcttatttcattatggtgaaagttggaacctcttacgtgcccgatcaactcgagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggcagaatttcagataaaaaaaatccttagctttcgctaaggatgatttctggaattcggtctcg - - - - Cir_qKqs_sequence - - CGAGaccctgcagtccggcaaaaaagggcaaggtgtcaccaccctgccctttttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccacaggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagctcgaggcttggattctcaccaataaaaaacgcccggcggcaaccgagcgttctgaacaaatccagatggagttctgaggtcattactggatctatcaacaggagtccaagcgagctcgatatcaaattacgccccgccctgccactcatcgcagtactgttgtaattcattaagcattctgccgacatggaagccatcacaaacggcatgatgaacctgaatcgccagcggcatcagcaccttgtcgccttgcgtataatatttgcccatggtgaaaacgggggcgaagaagttgtccatattggccacgtttaaatcaaaactggtgaaactcacccagggattggctgagacgaaaaacatattctcaataaaccctttagggaaataggccaggttttcaccgtaacacgccacatcttgcgaatatatgtgtagaaactgccggaaatcgtcgtggtattcactccagagcgatgaaaacgtttcagtttgctcatggaaaacggtgtaacaagggtgaacactatcccatatcaccagctcaccgtcttcattgccatacgaaattccggatgagcattcatcaggcgggcaagaatgtgaataaaggccggataaaacttgtgcttatttttctttacggtctttaaaaaggccgtaatatccagctgaacggtctggttataggtacattgagcaactgactgaaatgcctcaaaatgttctttacgatgccattgggatatatcaacggtggtatatccagtgatttttttctccattttagcttccttagctcctgaaaatctcgataactcaaaaaatacgcccggtagtgatcttatttcattatggtgaaagttggaacctcttacgtgcccgatcaactcgagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggcagaatttcagataaaaaaaatccttagctttcgctaaggatgatttctggaattcggtctcg - - - - - - tttacagctagctcagtcctaggtattatgctagc - J23101_sequence - - - GGAG - - - Scar_A_sequence - - - - Scar_B_sequence - TACT - - - - Cir_qKqs_Layout - - - - - - - module1_Layout - - - - 457.0 - j0nju1Eb_56 - 100.0 - 695.0 - 152.0 - - - - - - - 100.0 - 51.0 - 0.0 - 50.0 - J23101_3 - - - - j0nju1Eb_Layout - - - 1.0 - 50.0 - 0.0 - 100.0 - Scar_A_2 - - - - - - - 50.0 - Scar_B_4 - 101.0 - 100.0 - 0.0 - - - - - 152.0 - 100.0 - container - 695.0 - 457.0 - - - - - - backbone - 50.0 - 0.0 - 152.0 - 1.0 - - - - - 0.0 - 1.0 - 151.0 - Cir_qKqs_5 - 100.0 - - - - - - - - - Scar_A_Layout - - - - - Scar_B_Layout - - - - - J23101_Layout - - From 0d4996f1495508fc49caa65c2471e76cef89590a Mon Sep 17 00:00:00 2001 From: Gonzalo Vidal <35148159+Gonza10V@users.noreply.github.com> Date: Thu, 17 Apr 2025 15:14:46 -0600 Subject: [PATCH 3/6] Delete new_promoter_test.xml --- new_promoter_test.xml | 254 ------------------------------------------ 1 file changed, 254 deletions(-) delete mode 100644 new_promoter_test.xml diff --git a/new_promoter_test.xml b/new_promoter_test.xml deleted file mode 100644 index 1e805bd..0000000 --- a/new_promoter_test.xml +++ /dev/null @@ -1,254 +0,0 @@ - - - - - - - - - - three_prime_oh_location - - 43 - 40 - 1 - - - three_prime_overhang - 1 - - - - - - - - UJHDBOTD_70_five_prime_oh_component - 1 - - - - - - - - - 1 - UJHDBOTD_70_part - - - 1 - 39 - - 5 - - UJHDBOTD_70_part_location - - - - - - - - - 1 - - J23101_3 - - - - - - - - - 1 - five_prime_overhang - - - 1 - 1 - 4 - five_prime_oh_location - - - - - - - UJHDBOTD_70_extracted_part - - - - UJHDBOTD_70_three_prime_oh_component - 1 - - - - - - 1 - - - 1 - J23101 - J23101 - - - - - - - - - - UJHDBOTD_70_three_prime_oh - - 1 - - - - - Scar_B - - Scar_B - 1 - - - - - 1 - - - UJHDBOTD_70_five_prime_oh - - - - 1 - - Scar_A - - Scar_A - - - - - UJHDBOTD_70_extracted_part_seq - 1 - - - GGAGtttacagctagctcagtcctaggtattatgctagcTACT - - - J23101_sequence - tttacagctagctcagtcctaggtattatgctagc - - - - - 1 - - - UJHDBOTD_70_three_prime_oh_sequence - TACT - - - Scar_B_sequence - - - TACT - - - GGAG - UJHDBOTD_70_five_prime_oh_sequence - 1 - - - - - - - Scar_A_sequence - GGAG - - - - - - - - BsaI_enzyme - 1 - - - - - - - - 1 - - - restriction - - - - UJHDBOTD_70_asssembly_plan_interaction - 1 - - - - - 1 - - - UJHDBOTD_70_reactant_participation - - - - - - 1 - - UJHDBOTD_70_product_participation - - - - - - - - - - 1 - - - - - UJHDBOTD_70_reaction_component - - - - - 1 - - - - - UJHDBOTD_70_reactant_component - - - - - - - UJHDBOTD_70_product_component - - 1 - - - - 1 - insert_assembly_plan - - From 041de0fdd9a14f435ae40b73f05a0cd6ae1cb6a4 Mon Sep 17 00:00:00 2001 From: Gonzalo Vidal <35148159+Gonza10V@users.noreply.github.com> Date: Thu, 17 Apr 2025 15:15:05 -0600 Subject: [PATCH 4/6] Delete new_bb_test.xml --- new_bb_test.xml | 256 ------------------------------------------------ 1 file changed, 256 deletions(-) delete mode 100644 new_bb_test.xml diff --git a/new_bb_test.xml b/new_bb_test.xml deleted file mode 100644 index 76ee58a..0000000 --- a/new_bb_test.xml +++ /dev/null @@ -1,256 +0,0 @@ - - - - - - UJHDBOTD_159_backbone - - - UJHDBOTD_159_backbone_location - 5 - - - 2199 - 1 - - - - 1 - - - - - - - Cir_qxow_5 - - - - 1 - - - - - - - 1 - five_prime_overhang - - - five_prime_oh_location - 4 - 1 - 1 - - - - - - - - - - - three_prime_overhang - - - - 2200 - three_prime_oh_location - 2203 - 1 - - - - 1 - - - - UJHDBOTD_extracted_backbone - - - - - 1 - UJHDBOTD_159_three_prime_oh_component - - - - - - UJHDBOTD_159_five_prime_oh_component - 1 - - - - - - - - 1 - - - - UJHDBOTD_159_five_prime_oh - - 1 - - - - - Scar_F - 1 - - Scar_F - - - - - - Cir_qxow - Cir - - - - 1 - - - - - UJHDBOTD_159_three_prime_oh - 1 - - - - - - Scar_A - - - - - Scar_A - 1 - - - - - 1 - UJHDBOTD_extracted_backbone_seq - cgctgcatgaagagcctgcagtccggcaaaaaagggcaaggtgtcaccaccctgccctttttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccacaggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagctcgagtcccgtcaagtcagcgtaatgctctgccagtgttacaaccaattaaccaattctgattagaaaaactcatcgagcatcaaatgaaactgcaatttattcatatcaggattatcaataccatatttttgaaaaagccgtttctgtaatgaaggagaaaactcaccgaggcagttccataggatggcaagatcctggtatcggtctgcgattccgactcgtccaacatcaatacaacctattaatttcccctcgtcaaaaataaggttatcaagtgagaaatcaccatgagtgacgactgaatccggtgagaatggcaaaagcttatgcatttctttccagacttgttcaacaggccagccattacgctcgtcatcaaaatcactcgcatcaaccaaaccgttattcattcgtgattgcgcctgagcgagacgaaatacgcgatcgctgttaaaaggacaattacaaacaggaatcgaatgcaaccggcgcaggaacactgccagcgcatcaacaatattttcacctgaatcaggatattcttctaatacctggaatgctgttttcccggggatcgcagtggtgagtaaccatgcatcatcaggagtacggataaaatgcttgatggtcggaagaggcataaattccgtcagccagtttagtctgaccatctcatctgtaacatcattggcaacgctacctttgccatgtttcagaaacaactctggcgcatcgggcttcccatacaatcgatagattgtcgcacctgattgcccgacattatcgcgagcccatttatacccatataaatcagcatccatgttggaatttaatcgcggcctggagcaagacgtttcccgttgaatatggctcataacaccccttgtattactgtttatgtaagcagacagttttattgttcatgatgatatatttttatcttgtgcaatgtaacatcagagattttgagacacaacgtggctttgttgaataaatcgaacttttgctgagttgaaggatcagctcgagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggcagaatttcagataaaaaaaatccttagctttcgctaaggatgatttctggaattcgctcttcaatgggag - - - - cgct - 1 - UJHDBOTD_159_five_prime_oh_sequence - - - - - cgct - - - Scar_F_sequence - - - Cir_qxow_sequence - - - gcatgaagagcctgcagtccggcaaaaaagggcaaggtgtcaccaccctgccctttttctttaaaaccgaaaagattacttcgcgttatgcaggcttcctcgctcactgactcgctgcgctcggtcgttcggctgcggcgagcggtatcagctcactcaaaggcggtaatacggttatccacagaatcaggggataacgcaggaaagaacatgtgagcaaaaggccagcaaaaggccaggaaccgtaaaaaggccgcgttgctggcgtttttccacaggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaagaacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagaagatcctttgatcttttctacggggtctgacgctcagtggaacgaaaactcacgttaagggattttggtcatgagattatcaaaaaggatcttcacctagatccttttaaattaaaaatgaagttttaaatcaatctaaagtatatatgagtaaacttggtctgacagctcgagtcccgtcaagtcagcgtaatgctctgccagtgttacaaccaattaaccaattctgattagaaaaactcatcgagcatcaaatgaaactgcaatttattcatatcaggattatcaataccatatttttgaaaaagccgtttctgtaatgaaggagaaaactcaccgaggcagttccataggatggcaagatcctggtatcggtctgcgattccgactcgtccaacatcaatacaacctattaatttcccctcgtcaaaaataaggttatcaagtgagaaatcaccatgagtgacgactgaatccggtgagaatggcaaaagcttatgcatttctttccagacttgttcaacaggccagccattacgctcgtcatcaaaatcactcgcatcaaccaaaccgttattcattcgtgattgcgcctgagcgagacgaaatacgcgatcgctgttaaaaggacaattacaaacaggaatcgaatgcaaccggcgcaggaacactgccagcgcatcaacaatattttcacctgaatcaggatattcttctaatacctggaatgctgttttcccggggatcgcagtggtgagtaaccatgcatcatcaggagtacggataaaatgcttgatggtcggaagaggcataaattccgtcagccagtttagtctgaccatctcatctgtaacatcattggcaacgctacctttgccatgtttcagaaacaactctggcgcatcgggcttcccatacaatcgatagattgtcgcacctgattgcccgacattatcgcgagcccatttatacccatataaatcagcatccatgttggaatttaatcgcggcctggagcaagacgtttcccgttgaatatggctcataacaccccttgtattactgtttatgtaagcagacagttttattgttcatgatgatatatttttatcttgtgcaatgtaacatcagagattttgagacacaacgtggctttgttgaataaatcgaacttttgctgagttgaaggatcagctcgagtgccacctgacgtctaagaaaccattattatcatgacattaacctataaaaataggcgtatcacgaggcagaatttcagataaaaaaaatccttagctttcgctaaggatgatttctggaattcgctcttcaatg - - - - - - UJHDBOTD_159_three_prime_oh_sequence - 1 - ggag - - - Scar_A_sequence - ggag - - - - - bb_assembly_plan - - - - - 1 - - BsaI_enzyme - - - - - - UJHDBOTD_backbone_reactant_component - 1 - - - - - - - - - - - - - - UJHDBOTD_backbone_product_participation - 1 - - - 1 - - - - - - - UJHDBOTD_backbone_reactant_participation - 1 - - - - - - 1 - restriction - - - - - asssembly_plan_interaction - - - - - - - UJHDBOTD_backbone_reaction_component - 1 - - - - - - 1 - - - UJHDBOTD_backbone_product_component - 1 - - - - - - - - - From a6598fccbc2acf142fa341d43fe6935fc37d0592 Mon Sep 17 00:00:00 2001 From: Ryan Greer Date: Thu, 24 Apr 2025 11:18:58 -0600 Subject: [PATCH 5/6] documentation tutorials & readme --- README.md | 19 ++++++++++++++- docs/Installation.rst | 2 -- docs/Tutorials.rst | 36 +++++++++++++++++++++++++++- docs/index.rst | 11 ++++++++- notebooks/test_notebook.ipynb | 44 ++++++++++++++++++++++++++++++++++- 5 files changed, 106 insertions(+), 6 deletions(-) delete mode 100644 docs/Installation.rst diff --git a/README.md b/README.md index 403b029..ff28bea 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,19 @@ # SBOL2Build -SBOL2 utility functions to support build plan +SBOL2Build is a Python library for assisting in the planning, documentation, and distribution of DNA assembly plans using the Synthetic Biology Open Language 2.3 data standard. + +It was developed to support build functionality and workflows in SynBioSuite, based off the SBOL Best Practices. + + + +![PyPI - Version](https://img.shields.io/pypi/v/sbol2build) +[![Documentation Status](https://readthedocs.org/projects/sbol2build/badge/?version=latest)](https://sbol2build.readthedocs.io/en/latest/?badge=latest) +![PyPI - Python Version](https://img.shields.io/pypi/pyversions/sbol2build) +![PyPI - License](https://img.shields.io/pypi/l/sbol2build) +![gh-action badge](https://github.com/MyersResearchGroup/sbol2build/workflows/Python%20package/badge.svg) + +## Installing SBOL2Build: +```pip install sbol2build``` + +## Documentation + + Please visit the documentation with API reference and tutorials at Read the Docs: [sbol2build.rtfd.io](https://sbol2build.readthedocs.io) \ No newline at end of file diff --git a/docs/Installation.rst b/docs/Installation.rst deleted file mode 100644 index dbc9b80..0000000 --- a/docs/Installation.rst +++ /dev/null @@ -1,2 +0,0 @@ -Installation -====================================== \ No newline at end of file diff --git a/docs/Tutorials.rst b/docs/Tutorials.rst index 8da6e92..9e25bb6 100644 --- a/docs/Tutorials.rst +++ b/docs/Tutorials.rst @@ -1,3 +1,37 @@ Tutorials ====================================== -Let's get started with creating DNA assembly plans. First we will demonstrate a workflow using plasmid files from `SBOLCanvas `_: \ No newline at end of file +Let's get started with creating DNA assembly plans. First we will demonstrate a workflow using plasmid files from `SBOLCanvas `_: + +.. code:: ipython3 + + import sbol2build as s2b + import sbol2 + +First, read your plasmid SBOL files into documents. + +.. code:: ipython3 + + promoter = sbol2.Document() + promoter.read('pro_in_bb.xml') + + rbs = sbol2.Document() + rbs.read('rbs_in_bb.xml') + + cds = sbol2.Document() + cds.read('cds_in_bb.xml') + + terminator = sbol2.Document() + terminator.read('terminator_in_bb.xml') + + backbone = sbol2.Document() + backbone.read('backbone.xml') + +Create golden gate assembly plan object with all the parts, the acceptor backbone, and restriction enzyme. + +.. code:: ipython3 + + assembly_doc = sbol2.Document() + + assembly_plan = s2b.golden_gate_assembly_plan('tutorial_assembly_plan', [promoter, rbs, cds, terminator], backbone, 'BsaI', assembly_doc) + + composites = assembly_plan.run() \ No newline at end of file diff --git a/docs/index.rst b/docs/index.rst index 225bc38..5669efb 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -15,9 +15,18 @@ It was developed to support build functionality and workflows in `SynBioSuite sbol2build) (2.2.2)\n", + "Requirement already satisfied: appdirs>=1.4.4 in /opt/miniconda3/lib/python3.12/site-packages (from pydna->sbol2build) (1.4.4)\n", + "Requirement already satisfied: networkx>=2.8.8 in /opt/miniconda3/lib/python3.12/site-packages (from pydna->sbol2build) (3.4.2)\n", + "Requirement already satisfied: prettytable>=3.5.0 in /opt/miniconda3/lib/python3.12/site-packages (from pydna->sbol2build) (3.12.0)\n", + "Requirement already satisfied: pydivsufsort>=0.0.14 in /opt/miniconda3/lib/python3.12/site-packages (from pydna->sbol2build) (0.0.18)\n", + "Requirement already satisfied: pyfiglet==0.8.post1 in /opt/miniconda3/lib/python3.12/site-packages (from pydna->sbol2build) (0.8.post1)\n", + "Requirement already satisfied: seguid>=0.0.5 in /opt/miniconda3/lib/python3.12/site-packages (from pydna->sbol2build) (0.1.0)\n", + "Requirement already satisfied: rdflib>=5.0 in /opt/miniconda3/lib/python3.12/site-packages (from sbol2->sbol2build) (7.1.3)\n", + "Requirement already satisfied: python-dateutil in /opt/miniconda3/lib/python3.12/site-packages (from sbol2->sbol2build) (2.9.0.post0)\n", + "Requirement already satisfied: deprecated in /opt/miniconda3/lib/python3.12/site-packages (from sbol2->sbol2build) (1.2.15)\n", + "Requirement already satisfied: lxml in /opt/miniconda3/lib/python3.12/site-packages (from sbol2->sbol2build) (5.3.0)\n", + "Requirement already satisfied: requests in /opt/miniconda3/lib/python3.12/site-packages (from sbol2->sbol2build) (2.32.3)\n", + "Requirement already satisfied: urllib3 in /opt/miniconda3/lib/python3.12/site-packages (from sbol2->sbol2build) (2.2.3)\n", + "Requirement already satisfied: packaging>=20.0 in /opt/miniconda3/lib/python3.12/site-packages (from sbol2->sbol2build) (24.1)\n", + "Requirement already satisfied: wcwidth in /opt/miniconda3/lib/python3.12/site-packages (from prettytable>=3.5.0->pydna->sbol2build) (0.2.5)\n", + "Requirement already satisfied: wheel in /opt/miniconda3/lib/python3.12/site-packages (from pydivsufsort>=0.0.14->pydna->sbol2build) (0.44.0)\n", + "Requirement already satisfied: pyparsing<4,>=2.1.0 in /opt/miniconda3/lib/python3.12/site-packages (from rdflib>=5.0->sbol2->sbol2build) (2.4.7)\n", + "Requirement already satisfied: wrapt<2,>=1.10 in /opt/miniconda3/lib/python3.12/site-packages (from deprecated->sbol2->sbol2build) (1.17.2)\n", + "Requirement already satisfied: six>=1.5 in /opt/miniconda3/lib/python3.12/site-packages (from python-dateutil->sbol2->sbol2build) (1.16.0)\n", + "Requirement already satisfied: charset-normalizer<4,>=2 in /opt/miniconda3/lib/python3.12/site-packages (from requests->sbol2->sbol2build) (3.3.2)\n", + "Requirement already satisfied: idna<4,>=2.5 in /opt/miniconda3/lib/python3.12/site-packages (from requests->sbol2->sbol2build) (3.7)\n", + "Requirement already satisfied: certifi>=2017.4.17 in /opt/miniconda3/lib/python3.12/site-packages (from requests->sbol2->sbol2build) (2024.8.30)\n" + ] + } + ], + "source": [ + "!pip install sbol2build" + ] + }, { "cell_type": "code", "execution_count": 1, @@ -11,7 +53,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ From f635cb282a98aa5175056af4f74a22711a9bfabc Mon Sep 17 00:00:00 2001 From: Ryan Greer <57278424+doublergreer@users.noreply.github.com> Date: Thu, 24 Apr 2025 11:21:16 -0600 Subject: [PATCH 6/6] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ff28bea..e48b782 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # SBOL2Build SBOL2Build is a Python library for assisting in the planning, documentation, and distribution of DNA assembly plans using the Synthetic Biology Open Language 2.3 data standard. -It was developed to support build functionality and workflows in SynBioSuite, based off the SBOL Best Practices. +It was developed to support build functionality and workflows in [SynBioSuite](https://synbiosuite.org), based off the [SBOL Best Practices](https://github.com/SynBioDex/SBOL-examples/tree/main/SBOL/best-practices/BP011/). @@ -16,4 +16,4 @@ It was developed to support build functionality and workflows in SynBioSuite, ba ## Documentation - Please visit the documentation with API reference and tutorials at Read the Docs: [sbol2build.rtfd.io](https://sbol2build.readthedocs.io) \ No newline at end of file + Please visit the documentation with API reference and tutorials at Read the Docs: [sbol2build.rtfd.io](https://sbol2build.readthedocs.io)