update

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'")
-

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

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 
-[<f313c560442dc50108a0228a7cfc2c2b><f313c560442dc50108a0228a7cfc2c2b>]
+[<f137f01226224b6e36124c27289f4847><f137f01226224b6e36124c27289f4847>]
 % ReportLab generated PDF document -- digest (http://www.reportlab.com)
 
 /Info 6 0 R

plasmid_sequence.gb

@@ -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
-//