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Wrong circular alignment #335

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Wrong circular alignment #335

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Binary file added TN9W63_4_pREX0010.ab1
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11 changes: 11 additions & 0 deletions dummy.py
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from pydna.parsers import parse
from Bio.SeqIO import parse as bio_parse
from opencloning.dna_utils import align_sanger_traces

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with open('TN9W63_4_pREX0010.ab1', 'rb') as f:
trace = next(bio_parse(f, 'abi'))

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seq = parse('pREX0008_rc.gb')[0]

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aligned = align_sanger_traces(seq, [str(trace.seq)])
print(*aligned, sep='\n')

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225 changes: 225 additions & 0 deletions pREX0008_rc.gb
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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
//
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