diff --git a/TN9W63_4_pREX0010.ab1 b/TN9W63_4_pREX0010.ab1 new file mode 100644 index 0000000..3980154 Binary files /dev/null and b/TN9W63_4_pREX0010.ab1 differ diff --git a/dummy.py b/dummy.py new file mode 100644 index 0000000..d8c5faf --- /dev/null +++ b/dummy.py @@ -0,0 +1,11 @@ +from pydna.parsers import parse +from Bio.SeqIO import parse as bio_parse +from opencloning.dna_utils import align_sanger_traces + +with open('TN9W63_4_pREX0010.ab1', 'rb') as f: + trace = next(bio_parse(f, 'abi')) + +seq = parse('pREX0008_rc.gb')[0] + +aligned = align_sanger_traces(seq, [str(trace.seq)]) +print(*aligned, sep='\n') diff --git a/pREX0008_rc.gb b/pREX0008_rc.gb new file mode 100644 index 0000000..2dba103 --- /dev/null +++ b/pREX0008_rc.gb @@ -0,0 +1,225 @@ +LOCUS pREX0008_rc 4180 bp DNA circular SYN 20-JUN-2025 +DEFINITION pREX0008_rc. +ACCESSION 2_rc +VERSION 2_rc +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + CDS complement(171..1031) + /label="AmpR" + /note="pLannotate" + /database="snapgene" + /identity="99.8" + /match_length="100.0" + /fragment="False" + /other="CDS" + promoter complement(1032..1136) + /label="AmpR promoter" + /note="pLannotate" + /database="snapgene" + /identity="100.0" + /match_length="100.0" + /fragment="False" + /other="promoter" + CDS 1231..1266 + /label="rop (fragment)" + /note="pLannotate" + /database="snapgene" + /identity="100.0" + /match_length="18.8" + /fragment="True" + /other="CDS" + misc_feature 1368..1417 + /label="bom (fragment)" + /note="pLannotate" + /database="snapgene" + /identity="100.0" + /match_length="35.5" + /fragment="True" + /other="misc_feature" + rep_origin complement(1493..1873) + /label="M13 ori" + /note="pLannotate" + /database="snapgene" + /identity="100.0" + /match_length="100.0" + /fragment="False" + /other="rep_origin" + misc_feature 1892..1943 + /label="bom (fragment)" + /note="pLannotate" + /database="snapgene" + /identity="100.0" + /match_length="36.9" + /fragment="True" + /other="misc_feature" + CDS complement(1949..2072) + /label="lacZα (fragment)" + /note="pLannotate" + /database="snapgene" + /identity="100.0" + /match_length="71.3" + /fragment="True" + /other="CDS" + LTR complement(2074..2196) + /label="5' LTR (truncated) (fragment)" + /note="pLannotate" + /database="snapgene" + /identity="99.2" + /match_length="68.0" + /fragment="True" + /other="LTR" + CDS complement(2195..2222) + /label="lacZα (fragment)" + /note="pLannotate" + /database="snapgene" + /identity="100.0" + /match_length="16.1" + /fragment="True" + /other="CDS" + CDS complement(2308..2655) + /label="rev" + /note="pLannotate" + /database="swissprot" + /identity="100.0" + /match_length="100.0" + /fragment="False" + /other="CDS" + promoter complement(2741..2774) + /label="TRE3GV promoter (fragment)" + /note="pLannotate" + /database="snapgene" + /identity="100.0" + /match_length="9.7" + /fragment="True" + /other="promoter" + promoter complement(2784..3045) + /label="RSV promoter" + /note="pLannotate" + /database="snapgene" + /identity="100.0" + /match_length="100.0" + /fragment="False" + /other="promoter" + ncRNA complement(3081..3175) + /label="Retro dr1" + /note="pLannotate" + /database="Rfam" + /identity="100.0" + /match_length="105.6" + /fragment="False" + /other="ncRNA" + protein_bind complement(3214..3230) + /label="lac operator" + /note="pLannotate" + /database="snapgene" + /identity="100.0" + /match_length="100.0" + /fragment="False" + /other="protein_bind" + promoter complement(3238..3268) + /label="lac promoter" + /note="pLannotate" + /database="snapgene" + /identity="100.0" + /match_length="100.0" + /fragment="False" + /other="promoter" + protein_bind complement(3283..3304) + /label="CAP binding site" + /note="pLannotate" + /database="snapgene" + /identity="100.0" + /match_length="100.0" + /fragment="False" + /other="protein_bind" + CDS complement(3317..3409) + /label="lacI (fragment)" + /note="pLannotate" + /database="snapgene" + /identity="100.0" + /match_length="8.6" + /fragment="True" + /other="CDS" + rep_origin complement(3592..4180) + /label="ori" + /note="pLannotate" + /database="snapgene" + /identity="99.8" + /match_length="100.0" + /fragment="False" + /other="rep_origin" +ORIGIN + 1 gaagatcctt tgatcttttc tacggggtct gacgctcagt ggaacgaaaa ctcacgttaa + 61 gggattttgg tcatgagatt atcaaaaagg atcttcacct agatcctttt aaattaaaaa + 121 tgaagtttta aatcaatcta aagtatatat gagtaaactt ggtctgacag ttaccaatgc + 181 ttaatcagtg aggcacctat ctcagcgatc tgtctatttc gttcatccat agttgcctga + 241 ctccccgtcg tgtagataac tacgatacgg gagggcttac catctggccc cagtgctgca + 301 atgataccgc gagacccacg ctcaccggct ccagatttat cagcaataaa ccagccagcc + 361 ggaagggccg agcgcagaag tggtcctgca actttatccg cctccatcca gtctattaat + 421 tgttgccggg aagctagagt aagtagttcg ccagttaata gtttgcgcaa cgttgttgcc + 481 attgctacag gcatcgtggt gtcacgctcg tcgtttggta tggcttcatt cagctccggt + 541 tcccaacgat caaggcgagt tacatgatcc cccatgttgt gcaaaaaagc ggttagctcc + 601 ttcggtcctc cgatcgttgt cagaagtaag ttggccgcag tgttatcact catggttatg + 661 gcagcactgc ataattctct tactgtcatg ccatccgtaa gatgcttttc tgtgactggt + 721 gagtactcaa ccaagtcatt ctgagaatag tgtatgcggc gaccgagttg ctcttgcccg + 781 gcgtcaatac gggataatac cgcgccacat agcagaactt taaaagtgct catcattgga + 841 aaacgttctt cggggcgaaa actctcaagg atcttaccgc tgttgagatc cagttcgatg + 901 taacccactc gtgcacccaa ctgatcttca gcatctttta ctttcaccag cgtttctggg + 961 tgagcaaaaa caggaaggca aaatgccgca aaaaagggaa taagggcgac acggaaatgt + 1021 tgaatactca tactcttcct ttttcaatat tattgaagca tttatcaggg ttattgtctc + 1081 atgagcggat acatatttga atgtatttag aaaaataaac aaataggggt tccgcgcaca + 1141 tttccccgaa aagtgccacc tgacgtctaa gaaaccatta ttatcatgac attaacctat + 1201 aaaaataggc gtatcacgag gccctttcgt ctcgcgcgtt tcggtgatga cggtgaaaac + 1261 ctctgacaca tgcagctccc ggagacggtc acagcttgtc tgtaagcgga tgccgggagc + 1321 agacaagccc gtcagggcgc gtcagcgggt gttggcgggt gtcggggctg gcttaactat + 1381 gcggcatcag agcagattgt actgagagtg caccataaaa ttgtaaacgt taatattttg + 1441 ttaaaattcg cgttaaattt ttgttaaatc agctcatttt ttaaccaata ggccgaaatc + 1501 ggcaaaatcc cttataaatc aaaagaatag cccgagatag ggttgagtgt tgttccagtt + 1561 tggaacaaga gtccactatt aaagaacgtg gactccaacg tcaaagggcg aaaaaccgtc + 1621 tatcagggcg atggcccact acgtgaacca tcacccaaat caagtttttt ggggtcgagg + 1681 tgccgtaaag cactaaatcg gaaccctaaa gggagccccc gatttagagc ttgacgggga + 1741 aagccggcga acgtggcgag aaaggaaggg aagaaagcga aaggagcggg cgctagggcg + 1801 ctggcaagtg tagcggtcac gctgcgcgta accaccacac ccgccgcgct taatgcgccg + 1861 ctacagggcg cgtactatgg ttgctttgac gtatgcggtg tgaaataccg cacagatgcg + 1921 taaggagaaa ataccgcatc aggcgccatt cgccattcag gctgcgcaac tgttgggaag + 1981 ggcgatcggt gcgggcctct tcgctattac gccagctggc gaaaggggga tgtgctgcaa + 2041 ggcgattaag ttgggtaacg ccagggtttt cctgatctct agttaccaga gtcacacaac + 2101 agacgggcac acactacttg aagcactcaa ggcaagcttt attgaggctt aagcagtggg + 2161 ttccctagtt agccagagat ctcccaggct cagatcacga cgttgtaaaa cgacggccag + 2221 tgccaagctt cttgtactac ttctataacc ctatctgtcc cctcagctac tgctatagct + 2281 gtggcattga gcaagctaac agcactattc tttagctcct gactccaata ttgtaggaga + 2341 ttccaccaat atttgagggc ttcccacccc ctgcgtccca gaagttccac aatcctcgtt + 2401 acaatcaaga gtaagtctct caagcggtgg tagctgaaga ggcacaggct ccgcagatcg + 2461 tcccagataa gtgctaagga tccgttcact aatcgaatgg atctgtctct gtctctctct + 2521 ccaccttctt cttctattcc ttcgggcctg tcgggtcccc tcgggattgg gaggtgggtt + 2581 gctttgatag agaaacttga tgagtctgac tgccttgagg aggtcttcgt cgctgtctcc + 2641 gcttcttcct gccataggag atgcctaatc gactagcttc gaggggaggc tggatcggtc + 2701 ccggtgtctt ctatggaggt caaaacagcg tggatggcgt ctccaggcga tctgacggtt + 2761 cactaaacga gctcgagctt ggaggtgcac accaatgtgg tgaatggtca aatggcgttt + 2821 attgtatcga gctaggcact taaatacaat atctctgcaa tgcggaattc agtggttcgt + 2881 ccaatccatg tcagacccgt ctgttgcctt cctaataagg cacgatcgta ccaccttact + 2941 tccaccaatc ggcatgcacg gtgctttttc tctccttgta aggcatgttg ctaactcatc + 3001 gttaccatgt tgcaagacta caagagtatt gcataagact acatttcccc ctccctatgc + 3061 aaaagcgaaa ctactatatc ctgaggggac tcctaaccgc gtacaaccga agccccgctt + 3121 ttcgcctaaa cacaccctag tcccctcaga tacgcgtata tctggcccgt acatcgaatt + 3181 cgtaatcatg tcatagctgt ttcctgtgtg aaattgttat ccgctcacaa ttccacacaa + 3241 catacgagcc ggaagcataa agtgtaaagc ctggggtgcc taatgagtga gctaactcac + 3301 attaattgcg ttgcgctcac tgcccgcttt ccagtcggga aacctgtcgt gccagctgca + 3361 ttaatgaatc ggccaacgcg cggggagagg cggtttgcgt attgggcgct cttccgcttc + 3421 ctcgctcact gactcgctgc gctcggtcgt tcggctgcgg cgagcggtat cagctcactc + 3481 aaaggcggta atacggttat ccacagaatc aggggataac gcaggaaaga acatgtgagc + 3541 aaaaggccag caaaaggcca ggaaccgtaa aaaggccgcg ttgctggcgt ttttccatag + 3601 gctccgcccc cctgacgagc atcacaaaaa tcgacgctca agtcagaggt ggcgaaaccc + 3661 gacaggacta taaagatacc aggcgtttcc ccctggaagc tccctcgtgc gctctcctgt + 3721 tccgaccctg ccgcttaccg gatacctgtc cgcctttctc ccttcgggaa gcgtggcgct + 3781 ttctcatagc tcacgctgta ggtatctcag ttcggtgtag gtcgttcgct ccaagctggg + 3841 ctgtgtgcac gaaccccccg ttcagcccga ccgctgcgcc ttatccggta actatcgtct + 3901 tgagtccaac ccggtaagac acgacttatc gccactggca gcagccactg gtaacaggat + 3961 tagcagagcg aggtatgtag gcggtgctac agagttcttg aagtggtggc ctaactacgg + 4021 ctacactaga agaacagtat ttggtatctg cgctctgctg aagccagtta ccttcggaaa + 4081 aagagttggt agctcttgat ccggcaaaca aaccaccgct ggtagcggtg gtttttttgt + 4141 ttgcaagcag cagattacgc gcagaaaaaa aggatctcaa +//