From 9ad74c17458f9184c5f33623a54d0c7917ab8737 Mon Sep 17 00:00:00 2001 From: mpabi Date: Wed, 12 Jun 2024 12:27:18 +0200 Subject: [PATCH] update --- gfp-old.py | 29 ++++++++-- gfp2.py | 29 +++++++--- pdf/plasmid_map.pdf | 4 +- plasmid_sequence.gb | 131 -------------------------------------------- 4 files changed, 47 insertions(+), 146 deletions(-) delete mode 100644 plasmid_sequence.gb diff --git a/gfp-old.py b/gfp-old.py index 999a65e..dcbf9f9 100644 --- a/gfp-old.py +++ b/gfp-old.py @@ -8,11 +8,13 @@ import os from Bio import Entrez, SeqIO from Bio.Seq import Seq from Bio.SeqFeature import SeqFeature, FeatureLocation + from Bio.Restriction import RestrictionBatch, EcoRI, BamHI, HindIII +from Bio.Restriction import AllEnzymes, Analysis + from Bio.Graphics import GenomeDiagram from reportlab.lib import colors - #%% # Ustawienia Entrez Entrez.email = "your_email@example.com" # Wpisz swój adres email @@ -39,7 +41,11 @@ plasmid_file_path = 'plasmid_sequence.gb' # ID dla sekwencji w NCBI gfp_id = "U87974" -plasmid_id = "U96626" +#plasmid_id = "U96626" +plasmid_id = "M77789" #puc19 +#plasmid_id = "EF442785" #pet28 + +#%% # Sprawdzanie i pobieranie sekwencji GFP if not os.path.exists(gfp_file_path): @@ -54,6 +60,7 @@ else: gfp_seq = str(gfp_record.seq) print(f"GFP Sequence: {gfp_seq[:60]}...") +#%% # Sprawdzanie i pobieranie sekwencji plazmidu if not os.path.exists(plasmid_file_path): print(f"Plik {plasmid_file_path} nie istnieje. Pobieranie z serwera NCBI...") @@ -63,6 +70,7 @@ else: print(f"Plik {plasmid_file_path} istnieje. Wczytywanie danych z lokalnego pliku...") record = load_local_sequence(plasmid_file_path) print(f"Wczytano dane z pliku {plasmid_file_path}.") + #%% # Dodanie sekwencji kodującej His6 his6_tag = "CACCACCACCACCACCAC" # Sekwencja kodująca 6x histydynę (His6) @@ -79,15 +87,27 @@ reverse_primer = str(Seq(gfp_seq_with_his6[-20:]).reverse_complement()) # Ostat print(f"Forward Primer: {forward_primer}") print(f"Reverse Primer: {reverse_primer}") - #%% # Miejsca cięcia restryktazy enzymes = RestrictionBatch([EcoRI, BamHI, HindIII]) +#enzymes = RestrictionBatch([BamHI, ]) restriction_sites = enzymes.search(record.seq) +#%% +# Przeprowadzenie analizy restrykcyjnej +analysis = Analysis(AllEnzymes, record.seq) + +# Wynik analizy +results = analysis.full() + +# Wyświetlanie wyników +#for enzyme in results: +# if len(results[enzyme]) > 0: +# print(f"{enzyme}: {results[enzyme]}") + #%% # Utwórz diagram plazmidu -diagram = GenomeDiagram.Diagram("pET-28a(+) Plasmid Map") +diagram = GenomeDiagram.Diagram("PUC19 Plasmid Map") track = diagram.new_track(1, name="Annotated Features", greytrack=True) feature_set = track.new_set() @@ -138,4 +158,3 @@ diagram.draw(format="circular", circular=True, pagesize='A4', start=0, end=len(r diagram.write("pdf/plasmid_map.pdf", "PDF") print("Zapisano diagram plazmidu do pliku 'plasmid_map.pdf'") - diff --git a/gfp2.py b/gfp2.py index 4f522e8..e4b7d7c 100644 --- a/gfp2.py +++ b/gfp2.py @@ -91,6 +91,8 @@ for feature in record.features: print() + + #%% # Znajdź i wyświetl sekwencję terminatora T7 for feature in record.features: @@ -110,6 +112,25 @@ for feature in record.features: print() +#%% +t=record[25:73].seq + +#%% +a = str (t) + +#%% +class Rev: + def __init__ (self, seq=None): + self.seq = seq + + def rev (self): + pass + +#%% +r = Rev(a) + + + #%% # Sekwencja DNA @@ -169,14 +190,6 @@ def print_sticky_ends(seq1, sticky_end1, seq2, sticky_end2, start1, start2): print("Fragmenty po cięciu NcoI i Bpu1102I:") print_sticky_ends(ncoI_fragment[:-4], ncoI_sticky_end, bpu1102I_fragment[4:], bpu1102I_sticky_end, ncoI_site-16, bpu1102I_site) -#%% -# Dodanie sekwencji kodującej His6 -his6_tag = "CACCACCACCACCACCAC" # Sekwencja kodująca 6x histydynę (His6) - -#%% -# Sekwencja białka GFP z His6 tagiem na końcu -t = gfp_seq_with_his6 = gfp_seq + his6_tag - #%% # Projektowanie starterów forward_primer = gfp_seq[:20] # Pierwsze 20 nukleotydów sekwencji GFP diff --git a/pdf/plasmid_map.pdf b/pdf/plasmid_map.pdf index c79dc8e..9091c71 100644 --- a/pdf/plasmid_map.pdf +++ b/pdf/plasmid_map.pdf @@ -32,7 +32,7 @@ endobj endobj 6 0 obj << -/Author (anonymous) /CreationDate (D:20240609165346+00'00') /Creator (ReportLab PDF Library - www.reportlab.com) /Keywords () /ModDate (D:20240609165346+00'00') /Producer (ReportLab PDF Library - www.reportlab.com) +/Author (anonymous) /CreationDate (D:20240610140644+00'00') /Creator (ReportLab PDF Library - www.reportlab.com) /Keywords () /ModDate (D:20240610140644+00'00') /Producer (ReportLab PDF Library - www.reportlab.com) /Subject (unspecified) /Title () /Trapped /False >> endobj @@ -62,7 +62,7 @@ xref trailer << /ID -[] +[] % ReportLab generated PDF document -- digest (http://www.reportlab.com) /Info 6 0 R diff --git a/plasmid_sequence.gb b/plasmid_sequence.gb deleted file mode 100644 index 772d2c8..0000000 --- a/plasmid_sequence.gb +++ /dev/null @@ -1,131 +0,0 @@ -LOCUS MMU96626 4742 bp DNA linear ROD 07-FEB-1998 -DEFINITION Mus musculus chondroadherin gene, complete cds. -ACCESSION U96626 -VERSION U96626.1 -KEYWORDS . -SOURCE Mus musculus (house mouse) - ORGANISM Mus musculus - Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; - Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; - Muroidea; Muridae; Murinae; Mus; Mus. -REFERENCE 1 (bases 1 to 4742) - AUTHORS Landgren,C., Beier,D.R., Fassler,R., Heinegard,D. and Sommarin,Y. - TITLE The mouse chondroadherin gene: characterization and chromosomal - localization - JOURNAL Genomics 47 (1), 84-91 (1998) - PUBMED 9465299 -REFERENCE 2 (bases 1 to 4742) - AUTHORS Landgren,C. and Sommarin,Y. - TITLE Direct Submission - JOURNAL Submitted (07-APR-1997) Connective Tissue, Cell and Molecular - Biology, Lund 22100, Sweden -FEATURES Location/Qualifiers - source 1..4742 - /organism="Mus musculus" - /mol_type="genomic DNA" - /db_xref="taxon:10090" - /chromosome="11" - /map="between D11Mit36 and D11Mit10" - mRNA join(671..1490,3420..3583,3831..3976,4202..4742) - /product="chondroadherin" - exon 671..1490 - /number=1 - CDS join(720..1490,3420..3583,3831..3972) - /codon_start=1 - /product="chondroadherin" - /protein_id="AAC39963.1" - /translation="MARALLFSLVFLAILLPALAACPQNCHCHGDLQHVICDKVGLQKI - PKVSETTKLLNLQRNNFPVLAANSFRTMPNLVSLHLQHCNIREVAAGAFRGLKQLIYLY - LSHNDIRVLRAGAFDDLTELTYLYLDHNKVSELPRGLLSPLVNLFILQLNNNKIRELRA - GAFQGAKDLRWLYLSENALSSLQPGSLDDVENLAKFHLDKNQLSSYPSAALSKLRVVEE - LKLSHNPLKSIPDNAFQSFGRYLETLWLDNTNLEKFSDAAFSGVTTLKHVHLDNNRLNQ - LPSSFPFDNLETLTLTNNPWKCTCQLRGLRRWLEAKASRPDATCSSPAKFKGQRIRDTD - ALRSCKSPTKRSKKAGRH" - exon 3420..3583 - /number=2 - exon 3831..3976 - /number=3 - exon 4202..4742 - /number=4 -ORIGIN - 1 gagctcttac gggcctggtg ccactgggct ccgagaaggg gcagagccaa acgcacggct - 61 gtcagctagc ctctgcaacc agctccccca cctccttggg ataaactgag gaacccagaa - 121 gcgggagccc aacccacagc agctctcacg ctccgcctgc gccgcacaac agtcccatta - 181 aagcgccgcc ggctggccga ccgcggtgag acgcatccgg ctgtcgggcc ccacttcctc - 241 cctcccggag tccagggtga cctgtctgcc aagggtgtat gggggaagga gacgtagaga - 301 actcaaactt gagcaaataa ataagttctg ggaacacttc cctctgccca gtggaaattc - 361 agaagcccct cgacacacct atcaccgtcc accccacctc ggggtgttgg tccagataga - 421 ggagggtagg ggaaggtgca gcataatgtt tgcaaacagg aaccaagggg ttggggttca - 481 ggggaagggc cctcagccct acacacggtc tcctgctgtg aaaagaggcc cccagccatc - 541 gaggatgggg acgcatctct gggcgggaag gggttaaatc agtggcttcg gtgctccacg - 601 tagtagctgg ctccgctgcc aactgcggtc aaggctgccc tataaatggg ccgggagacc - 661 cgagagtcga ggacttgtcg ctgccttagc ccccagccca ggctcaaggc gttctaacca - 721 tggcccgcgc gctcttattc agtctggtct ttcttgccat cctcctgcct gcgctagccg - 781 cctgccccca aaactgccac tgccatggag atctgcagca tgtcatctgc gacaaggtgg - 841 ggctgcagaa gatccccaag gtatcagaga caaccaaact gctcaatctc cagcgcaaca - 901 acttcccggt gctggctgcc aactcgtttc ggaccatgcc gaacctggtc tccctgcacc - 961 tgcaacactg caacatccgc gaggtggcgg ctggtgcctt ccgaggcctg aagcagctta - 1021 tctacctgta cctgtcccac aacgacatcc gggtattgcg agctggagcc ttcgacgacc - 1081 tgactgaact cacttacctc tatctagacc acaacaaagt gtcggaactg ccccgggggt - 1141 tgctctctcc tctggtcaac ctcttcatct tgcaactcaa caacaacaaa atccgagagc - 1201 tgcgtgctgg agctttccag ggggccaagg acctgcgctg gctctacctg tcagaaaatg - 1261 ccctcagttc cctgcagcct ggttccctgg atgatgtgga gaacctagcc aagttccacc - 1321 tggacaagaa ccagctgtct agctacccct cagccgccct gagcaaactt cgggtggtgg - 1381 aggagctgaa gctgtctcac aaccctctga agagcatccc agacaatgcc ttccagtcct - 1441 tcggtagata tctggagacc ctctggctgg ataacaccaa cctggagaag gtaagtgccc - 1501 cagctgcagt tctcccggct ctttctagga tgccacccca ggaaccacat cgggacagca - 1561 ttccctcctc ctggactcct tgtcactcag attatcctcc aaagcaaggg gcctttgcca - 1621 cttctctctg cattgacaca cacccctccc catccttctc acccttacct ggtcccgagg - 1681 cttctcagac agggctctct tgggactcct tgtaagagat ggaactgttc tggtcccaca - 1741 aatggcctct ggggaggcat ctgccccaga ccccacggtt aacagcagac acctcttcct - 1801 gttggacttt ccacccctct cttaccagtc tcctgcaagc ctaccatttc ataaaggaag - 1861 gtttgtctac tgaggcacct tccagaagct gagagaacac aaagagtgcc tgttcccagt - 1921 gggtgctggc ctgtgttgct aaggtaaagt gagaggccag aggatgaatt ggggagcagg - 1981 taccttaagg agaactctcc cacaccctcg tcccattccc tccgtgggtc gaaacacact - 2041 caattttatt gcaacctcgg gtcgatttca aatatggacg ggaaaccaag acacggagac - 2101 ctgacttggc ttcaccgagt tgctggcttg gtgctcttgc agcccgtgaa taaacacatg - 2161 caatccctgg cacacgcccc cccaagtgtc tcctcagagc acagactgac tgtctcactg - 2221 tccagcagac agtttgttga cttttgcttt ccccagtcac cagatcccag actcctcaat - 2281 tcttcctccc ttgggatgct caggctagcc tggtcggggc tgtctaggag caaagtcctt - 2341 ttcagggaat caccctggta cacaacacag tttcagccag aaggttcggg cagagaccag - 2401 agcgaggtag agtagttttg tttgtagaga acgtcacagc ccaatctggt ctgtgagagg - 2461 tcacagatac tgagctgagg acagaacgcc aaccttatct aggtagatgg agccttctgg - 2521 gtggatcttc tttagcctgg cctcacccca gctaaatgta gaccacccta gtgacaaaac - 2581 agtggccagt agaacagcat acgaaggctg atttagaatg aggaggccaa agccgggcgt - 2641 ggtagcgcac gccttcaatc ccagtacctg ggaggcaaag gcaggcgaat ttctaagttc - 2701 gaggccagcc tggtctacag agtgagttcc aggacagcca ggactacaca gagaaaccct - 2761 gtctcacaaa aaccaaaaag aaaaaagaaa aaaaaaagaa tgaggaggcc agagagaact - 2821 ggcaccaagg ctcagaggag ggcaccaata catttcctct ggagccatcc atcctggcca - 2881 aagtgcccac agagagctcc acaaatagca tctagcagaa ggcagagcaa tgaggacacc - 2941 actgggggaa atcctgggac cagggggctg tggggagcct gggctcactg cccatcccac - 3001 caaaccctga ccaggttcac cgtgtgcccg ccccaggcac actgcccatc ccaccaaaca - 3061 ctgaccaggt tcaccgtgtg cccgcccggg cactcaaagc caagctctgc ctgctcccca - 3121 gacccagtgt ttgtgcaggg aggtgctgcc taggaggtgg gggacagggt gtggtcctgc - 3181 agctactgtt tactagctag gtgaccctgt ccaaaggact gaaccttttc cgtttacaca - 3241 ttgggaagga ccccttccct ctctctctct ctctcaaaaa aaggtgttgt ggaggatgac - 3301 atcattgtgg ctcctcaaca ggccagggcg tgtgtccagg gaaaagacaa ccctggtcct - 3361 ctgagaaggg agccaggaga ctgagttgag gtgctcactc tgcctccctc acctcacagt - 3421 tctcagatgc tgccttctcg ggtgtgacca cactgaaaca cgtccatctg gacaacaacc - 3481 gcctgaacca actgccttcc tccttcccct ttgacaacct ggagaccctc actctcacca - 3541 acaacccatg gaaatgcacc tgccagctcc gtggccttcg gcggtgagaa tattcctcca - 3601 tataaccccc agactgccgt ccacatgaca gacggtccta gagtaggaca gcctggacat - 3661 cctagtcagc tacctagcat gtcgggtact gagtggttcc cttctctcat ttgtcaaatg - 3721 aagatgacaa ctccagatat ttctatggcc atagtccatc ccggtcactg tccctttccc - 3781 aagccttccc acccagcttt tccaagccca gcaactcttt gtctctgtag gtggttggaa - 3841 gccaaggctt ctcgaccgga tgctacctgc tcctcgccag ccaagttcaa gggtcagcgg - 3901 attcgtgaca cagatgccct tcgcagctgc aaatccccga ccaagaggtc caagaaagct - 3961 ggccgccatt aaacaggtgg gggctgggta gggaggccac cacggtctac ctttggaaat - 4021 tccagatggg gtgctgctat atcccatgac accacttccg gaggagcaat cagttccctg - 4081 tcttacaaga aaaggaggga ggacaggata acctctccca tggcttggcc taggacgtcc - 4141 atgggtccct ttaatgactc tgggtgactg gaatcctaat acccatcttc tctcactata - 4201 ggtcctgatc cagccagtcc tggcgactgc cttccgctgg agagactact gacgttccct - 4261 cccatcatcc acaccttctc ctacagcctc tgcggatgca cagcgctgcc ccgcccccgc - 4321 ccccacctag gtacatcctg gcaggggcac tgggctctct atcaccatcc cagctccacc - 4381 cagtggggtc ctaggaaaga cacagaatcc ctccccagcc actgtgtctg ggctctgcca - 4441 tggctccttt gagagaagct attgtagaac ctcctaccct ctgtccatcg gagctaaagc - 4501 gcagtggtca ttgggatgac cacgttatta ccaccttcct cggttccctc tgtccctgcc - 4561 atttggaaac aaacatcagg cccctgaccc accctgattg ccagaaagaa tttcaggccc - 4621 atgccccaac tctgccagtt cctgcctgcc aggacatgct accaggatac cagtagcgct - 4681 tggctgcata tccttcctgt ttgcgctcca gatttctata aacataaatg tatgtgtgtt - 4741 ca -//