update
This commit is contained in:
mpabi
parent
71bd8ecfb8
commit
9ad74c1745
29
gfp-old.py
29
gfp-old.py
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@ -8,11 +8,13 @@ import os
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from Bio import Entrez, SeqIO
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from Bio.Seq import Seq
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from Bio.SeqFeature import SeqFeature, FeatureLocation
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from Bio.Restriction import RestrictionBatch, EcoRI, BamHI, HindIII
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from Bio.Restriction import AllEnzymes, Analysis
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from Bio.Graphics import GenomeDiagram
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from reportlab.lib import colors
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#%%
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# Ustawienia Entrez
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Entrez.email = "your_email@example.com" # Wpisz swój adres email
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@ -39,7 +41,11 @@ plasmid_file_path = 'plasmid_sequence.gb'
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# ID dla sekwencji w NCBI
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gfp_id = "U87974"
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plasmid_id = "U96626"
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#plasmid_id = "U96626"
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plasmid_id = "M77789" #puc19
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#plasmid_id = "EF442785" #pet28
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#%%
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# Sprawdzanie i pobieranie sekwencji GFP
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if not os.path.exists(gfp_file_path):
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@ -54,6 +60,7 @@ else:
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gfp_seq = str(gfp_record.seq)
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print(f"GFP Sequence: {gfp_seq[:60]}...")
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#%%
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# Sprawdzanie i pobieranie sekwencji plazmidu
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if not os.path.exists(plasmid_file_path):
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print(f"Plik {plasmid_file_path} nie istnieje. Pobieranie z serwera NCBI...")
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@ -63,6 +70,7 @@ else:
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print(f"Plik {plasmid_file_path} istnieje. Wczytywanie danych z lokalnego pliku...")
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record = load_local_sequence(plasmid_file_path)
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print(f"Wczytano dane z pliku {plasmid_file_path}.")
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#%%
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# Dodanie sekwencji kodującej His6
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his6_tag = "CACCACCACCACCACCAC" # Sekwencja kodująca 6x histydynę (His6)
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@ -79,15 +87,27 @@ reverse_primer = str(Seq(gfp_seq_with_his6[-20:]).reverse_complement()) # Ostat
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print(f"Forward Primer: {forward_primer}")
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print(f"Reverse Primer: {reverse_primer}")
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#%%
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# Miejsca cięcia restryktazy
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enzymes = RestrictionBatch([EcoRI, BamHI, HindIII])
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#enzymes = RestrictionBatch([BamHI, ])
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restriction_sites = enzymes.search(record.seq)
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#%%
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# Przeprowadzenie analizy restrykcyjnej
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analysis = Analysis(AllEnzymes, record.seq)
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# Wynik analizy
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results = analysis.full()
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# Wyświetlanie wyników
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#for enzyme in results:
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# if len(results[enzyme]) > 0:
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# print(f"{enzyme}: {results[enzyme]}")
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#%%
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# Utwórz diagram plazmidu
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diagram = GenomeDiagram.Diagram("pET-28a(+) Plasmid Map")
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diagram = GenomeDiagram.Diagram("PUC19 Plasmid Map")
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track = diagram.new_track(1, name="Annotated Features", greytrack=True)
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feature_set = track.new_set()
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@ -138,4 +158,3 @@ diagram.draw(format="circular", circular=True, pagesize='A4', start=0, end=len(r
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diagram.write("pdf/plasmid_map.pdf", "PDF")
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print("Zapisano diagram plazmidu do pliku 'plasmid_map.pdf'")
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29
gfp2.py
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gfp2.py
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@ -91,6 +91,8 @@ for feature in record.features:
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print()
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#%%
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# Znajdź i wyświetl sekwencję terminatora T7
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for feature in record.features:
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@ -110,6 +112,25 @@ for feature in record.features:
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print()
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#%%
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t=record[25:73].seq
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#%%
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a = str (t)
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#%%
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class Rev:
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def __init__ (self, seq=None):
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self.seq = seq
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def rev (self):
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pass
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#%%
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r = Rev(a)
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#%%
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# Sekwencja DNA
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@ -169,14 +190,6 @@ def print_sticky_ends(seq1, sticky_end1, seq2, sticky_end2, start1, start2):
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print("Fragmenty po cięciu NcoI i Bpu1102I:")
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print_sticky_ends(ncoI_fragment[:-4], ncoI_sticky_end, bpu1102I_fragment[4:], bpu1102I_sticky_end, ncoI_site-16, bpu1102I_site)
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#%%
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# Dodanie sekwencji kodującej His6
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his6_tag = "CACCACCACCACCACCAC" # Sekwencja kodująca 6x histydynę (His6)
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#%%
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# Sekwencja białka GFP z His6 tagiem na końcu
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t = gfp_seq_with_his6 = gfp_seq + his6_tag
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#%%
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# Projektowanie starterów
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forward_primer = gfp_seq[:20] # Pierwsze 20 nukleotydów sekwencji GFP
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@ -32,7 +32,7 @@ endobj
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endobj
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6 0 obj
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<<
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/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)
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/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)
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/Subject (unspecified) /Title () /Trapped /False
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>>
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endobj
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@ -62,7 +62,7 @@ xref
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trailer
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<<
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/ID
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[<f313c560442dc50108a0228a7cfc2c2b><f313c560442dc50108a0228a7cfc2c2b>]
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[<f137f01226224b6e36124c27289f4847><f137f01226224b6e36124c27289f4847>]
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% ReportLab generated PDF document -- digest (http://www.reportlab.com)
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/Info 6 0 R
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@ -1,131 +0,0 @@
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LOCUS MMU96626 4742 bp DNA linear ROD 07-FEB-1998
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DEFINITION Mus musculus chondroadherin gene, complete cds.
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ACCESSION U96626
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VERSION U96626.1
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KEYWORDS .
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SOURCE Mus musculus (house mouse)
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ORGANISM Mus musculus
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Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
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Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
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Muroidea; Muridae; Murinae; Mus; Mus.
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REFERENCE 1 (bases 1 to 4742)
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AUTHORS Landgren,C., Beier,D.R., Fassler,R., Heinegard,D. and Sommarin,Y.
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TITLE The mouse chondroadherin gene: characterization and chromosomal
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localization
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JOURNAL Genomics 47 (1), 84-91 (1998)
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PUBMED 9465299
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REFERENCE 2 (bases 1 to 4742)
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AUTHORS Landgren,C. and Sommarin,Y.
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TITLE Direct Submission
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JOURNAL Submitted (07-APR-1997) Connective Tissue, Cell and Molecular
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Biology, Lund 22100, Sweden
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FEATURES Location/Qualifiers
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source 1..4742
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/organism="Mus musculus"
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/mol_type="genomic DNA"
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/db_xref="taxon:10090"
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/chromosome="11"
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/map="between D11Mit36 and D11Mit10"
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mRNA join(671..1490,3420..3583,3831..3976,4202..4742)
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/product="chondroadherin"
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exon 671..1490
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/number=1
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CDS join(720..1490,3420..3583,3831..3972)
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/codon_start=1
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/product="chondroadherin"
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/protein_id="AAC39963.1"
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/translation="MARALLFSLVFLAILLPALAACPQNCHCHGDLQHVICDKVGLQKI
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PKVSETTKLLNLQRNNFPVLAANSFRTMPNLVSLHLQHCNIREVAAGAFRGLKQLIYLY
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LSHNDIRVLRAGAFDDLTELTYLYLDHNKVSELPRGLLSPLVNLFILQLNNNKIRELRA
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GAFQGAKDLRWLYLSENALSSLQPGSLDDVENLAKFHLDKNQLSSYPSAALSKLRVVEE
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LKLSHNPLKSIPDNAFQSFGRYLETLWLDNTNLEKFSDAAFSGVTTLKHVHLDNNRLNQ
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LPSSFPFDNLETLTLTNNPWKCTCQLRGLRRWLEAKASRPDATCSSPAKFKGQRIRDTD
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ALRSCKSPTKRSKKAGRH"
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exon 3420..3583
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/number=2
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exon 3831..3976
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/number=3
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exon 4202..4742
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/number=4
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ORIGIN
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1 gagctcttac gggcctggtg ccactgggct ccgagaaggg gcagagccaa acgcacggct
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61 gtcagctagc ctctgcaacc agctccccca cctccttggg ataaactgag gaacccagaa
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121 gcgggagccc aacccacagc agctctcacg ctccgcctgc gccgcacaac agtcccatta
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181 aagcgccgcc ggctggccga ccgcggtgag acgcatccgg ctgtcgggcc ccacttcctc
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241 cctcccggag tccagggtga cctgtctgcc aagggtgtat gggggaagga gacgtagaga
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301 actcaaactt gagcaaataa ataagttctg ggaacacttc cctctgccca gtggaaattc
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361 agaagcccct cgacacacct atcaccgtcc accccacctc ggggtgttgg tccagataga
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421 ggagggtagg ggaaggtgca gcataatgtt tgcaaacagg aaccaagggg ttggggttca
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481 ggggaagggc cctcagccct acacacggtc tcctgctgtg aaaagaggcc cccagccatc
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541 gaggatgggg acgcatctct gggcgggaag gggttaaatc agtggcttcg gtgctccacg
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601 tagtagctgg ctccgctgcc aactgcggtc aaggctgccc tataaatggg ccgggagacc
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661 cgagagtcga ggacttgtcg ctgccttagc ccccagccca ggctcaaggc gttctaacca
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721 tggcccgcgc gctcttattc agtctggtct ttcttgccat cctcctgcct gcgctagccg
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781 cctgccccca aaactgccac tgccatggag atctgcagca tgtcatctgc gacaaggtgg
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841 ggctgcagaa gatccccaag gtatcagaga caaccaaact gctcaatctc cagcgcaaca
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901 acttcccggt gctggctgcc aactcgtttc ggaccatgcc gaacctggtc tccctgcacc
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961 tgcaacactg caacatccgc gaggtggcgg ctggtgcctt ccgaggcctg aagcagctta
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1021 tctacctgta cctgtcccac aacgacatcc gggtattgcg agctggagcc ttcgacgacc
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1081 tgactgaact cacttacctc tatctagacc acaacaaagt gtcggaactg ccccgggggt
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1141 tgctctctcc tctggtcaac ctcttcatct tgcaactcaa caacaacaaa atccgagagc
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1201 tgcgtgctgg agctttccag ggggccaagg acctgcgctg gctctacctg tcagaaaatg
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1261 ccctcagttc cctgcagcct ggttccctgg atgatgtgga gaacctagcc aagttccacc
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1321 tggacaagaa ccagctgtct agctacccct cagccgccct gagcaaactt cgggtggtgg
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1381 aggagctgaa gctgtctcac aaccctctga agagcatccc agacaatgcc ttccagtcct
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1441 tcggtagata tctggagacc ctctggctgg ataacaccaa cctggagaag gtaagtgccc
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1501 cagctgcagt tctcccggct ctttctagga tgccacccca ggaaccacat cgggacagca
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1561 ttccctcctc ctggactcct tgtcactcag attatcctcc aaagcaaggg gcctttgcca
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1621 cttctctctg cattgacaca cacccctccc catccttctc acccttacct ggtcccgagg
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1681 cttctcagac agggctctct tgggactcct tgtaagagat ggaactgttc tggtcccaca
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1741 aatggcctct ggggaggcat ctgccccaga ccccacggtt aacagcagac acctcttcct
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1801 gttggacttt ccacccctct cttaccagtc tcctgcaagc ctaccatttc ataaaggaag
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1861 gtttgtctac tgaggcacct tccagaagct gagagaacac aaagagtgcc tgttcccagt
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1921 gggtgctggc ctgtgttgct aaggtaaagt gagaggccag aggatgaatt ggggagcagg
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1981 taccttaagg agaactctcc cacaccctcg tcccattccc tccgtgggtc gaaacacact
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2041 caattttatt gcaacctcgg gtcgatttca aatatggacg ggaaaccaag acacggagac
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2101 ctgacttggc ttcaccgagt tgctggcttg gtgctcttgc agcccgtgaa taaacacatg
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2161 caatccctgg cacacgcccc cccaagtgtc tcctcagagc acagactgac tgtctcactg
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2221 tccagcagac agtttgttga cttttgcttt ccccagtcac cagatcccag actcctcaat
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2281 tcttcctccc ttgggatgct caggctagcc tggtcggggc tgtctaggag caaagtcctt
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2341 ttcagggaat caccctggta cacaacacag tttcagccag aaggttcggg cagagaccag
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2401 agcgaggtag agtagttttg tttgtagaga acgtcacagc ccaatctggt ctgtgagagg
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2461 tcacagatac tgagctgagg acagaacgcc aaccttatct aggtagatgg agccttctgg
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2521 gtggatcttc tttagcctgg cctcacccca gctaaatgta gaccacccta gtgacaaaac
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2581 agtggccagt agaacagcat acgaaggctg atttagaatg aggaggccaa agccgggcgt
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2641 ggtagcgcac gccttcaatc ccagtacctg ggaggcaaag gcaggcgaat ttctaagttc
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2701 gaggccagcc tggtctacag agtgagttcc aggacagcca ggactacaca gagaaaccct
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2761 gtctcacaaa aaccaaaaag aaaaaagaaa aaaaaaagaa tgaggaggcc agagagaact
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2821 ggcaccaagg ctcagaggag ggcaccaata catttcctct ggagccatcc atcctggcca
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2881 aagtgcccac agagagctcc acaaatagca tctagcagaa ggcagagcaa tgaggacacc
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2941 actgggggaa atcctgggac cagggggctg tggggagcct gggctcactg cccatcccac
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3001 caaaccctga ccaggttcac cgtgtgcccg ccccaggcac actgcccatc ccaccaaaca
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3061 ctgaccaggt tcaccgtgtg cccgcccggg cactcaaagc caagctctgc ctgctcccca
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3121 gacccagtgt ttgtgcaggg aggtgctgcc taggaggtgg gggacagggt gtggtcctgc
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3181 agctactgtt tactagctag gtgaccctgt ccaaaggact gaaccttttc cgtttacaca
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3241 ttgggaagga ccccttccct ctctctctct ctctcaaaaa aaggtgttgt ggaggatgac
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3301 atcattgtgg ctcctcaaca ggccagggcg tgtgtccagg gaaaagacaa ccctggtcct
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3361 ctgagaaggg agccaggaga ctgagttgag gtgctcactc tgcctccctc acctcacagt
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3421 tctcagatgc tgccttctcg ggtgtgacca cactgaaaca cgtccatctg gacaacaacc
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3481 gcctgaacca actgccttcc tccttcccct ttgacaacct ggagaccctc actctcacca
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3541 acaacccatg gaaatgcacc tgccagctcc gtggccttcg gcggtgagaa tattcctcca
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3601 tataaccccc agactgccgt ccacatgaca gacggtccta gagtaggaca gcctggacat
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3661 cctagtcagc tacctagcat gtcgggtact gagtggttcc cttctctcat ttgtcaaatg
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3721 aagatgacaa ctccagatat ttctatggcc atagtccatc ccggtcactg tccctttccc
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3781 aagccttccc acccagcttt tccaagccca gcaactcttt gtctctgtag gtggttggaa
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3841 gccaaggctt ctcgaccgga tgctacctgc tcctcgccag ccaagttcaa gggtcagcgg
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3901 attcgtgaca cagatgccct tcgcagctgc aaatccccga ccaagaggtc caagaaagct
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3961 ggccgccatt aaacaggtgg gggctgggta gggaggccac cacggtctac ctttggaaat
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4021 tccagatggg gtgctgctat atcccatgac accacttccg gaggagcaat cagttccctg
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4081 tcttacaaga aaaggaggga ggacaggata acctctccca tggcttggcc taggacgtcc
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4141 atgggtccct ttaatgactc tgggtgactg gaatcctaat acccatcttc tctcactata
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4201 ggtcctgatc cagccagtcc tggcgactgc cttccgctgg agagactact gacgttccct
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4261 cccatcatcc acaccttctc ctacagcctc tgcggatgca cagcgctgcc ccgcccccgc
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4321 ccccacctag gtacatcctg gcaggggcac tgggctctct atcaccatcc cagctccacc
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4381 cagtggggtc ctaggaaaga cacagaatcc ctccccagcc actgtgtctg ggctctgcca
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4441 tggctccttt gagagaagct attgtagaac ctcctaccct ctgtccatcg gagctaaagc
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4501 gcagtggtca ttgggatgac cacgttatta ccaccttcct cggttccctc tgtccctgcc
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4561 atttggaaac aaacatcagg cccctgaccc accctgattg ccagaaagaa tttcaggccc
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4621 atgccccaac tctgccagtt cctgcctgcc aggacatgct accaggatac cagtagcgct
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4681 tggctgcata tccttcctgt ttgcgctcca gatttctata aacataaatg tatgtgtgtt
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4741 ca
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//
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