biolab 1.0.0

package/1.py

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+from Bio.Seq import Seq
+
+seq1=Seq("AGCTAGTAGCTGACGATCGATCGATCGCT")
+seq2=Seq("AGTCGTCGTCAGGATCGATCGTCGA")
+sliced=seq1[3:11]
+concat=sliced+seq2
+trans=sliced.transcribe()
+translate=concat.translate()
+print(sliced)
+print(concat)
+print(trans,  translate)

package/100.py

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+from Bio.PDB import PDBParser,PDBList
+import matplotlib.pyplot as plt
+from mpl_toolkits.mplot3d import Axes3D
+import numpy as np
+
+pdb_id="1A3N"
+pdb_list=PDBList()
+filepath=pdb_list.retrieve_pdb_file(pdb_id,pdir=".",file_format="pdb")
+pdpp=PDBParser(QUIET=True)
+structure =pdpp.get_structure(pdb_id,filepath)
+
+coords=[atom.coord for atom in structure.get_atoms()]
+coords=np.array(coords)
+
+fig=plt.figure()
+ax=fig.add_subplot(111,projection="3d")
+ax.scatter(coords[:,0],coords[:,1],coords[:,2],c="blue",s=10)
+plt.show()

package/2.py

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+from Bio import SeqIO
+
+
+def readf(fasta_file):
+        for records in SeqIO.parse(fasta_file,"fasta"):
+            print(f"{records.description}")
+
+
+
+fasta_file="fasta_1 (1).fasta"
+readf(fasta_file)

package/3.py

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+from Bio.Seq import Seq
+from Bio import SeqIO
+from Bio.SeqRecord import SeqRecord
+
+# Define the sequence
+seq1 = Seq("AGTCTGACTAACGATGCGTACGT")
+
+# Create the SeqRecord
+record = SeqRecord(
+    seq1,
+    id="1",
+    name="svscv",
+    description="Example DNA sequence",
+    annotations={
+        "molecule_type": "DNA",
+        "organism": "Unknown organism"
+    }
+)
+
+
+
+# Write to GenBank file
+file_path = "genbank.gb"
+with open(file_path, "w") as f:
+    SeqIO.write(record, f, "genbank")
+
+# Read back and print
+with open(file_path, "r") as f:
+    read_record = SeqIO.read(f, "genbank")
+
+print(read_record)

package/4.py

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+from Bio import Seq
+from Bio.Seq import Seq
+from Bio import SeqIO
+from Bio.SeqRecord import SeqRecord
+
+fasta="fasta_1 (1).fasta"
+with open(fasta,"r") as f:
+    records=[]
+    for record in SeqIO.parse(f,"fasta"):
+        seq=record.seq
+        des=record.description
+
+        re=SeqRecord(
+            seq,
+            id="1",
+            name="wfew",
+            description=des,
+            annotations={
+                "gene": "DNA",
+                "molecule_type":"DNA",
+                "function":"dssadc",
+                "organism":"unknown organism"
+            }
+        )
+        records.append(re)
+
+
+with open("genbank.gb","w") as ge:
+    SeqIO.write(records,ge,"genbank")
+
+
+
+

package/5.py

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+from Bio.SeqRecord import SeqRecord
+from Bio.SeqFeature import SeqFeature,FeatureLocation
+from Bio.Seq import Seq
+
+seq1=Seq("ATCGATGTGCATCGTACCGATCGCAGT")
+
+record=SeqRecord(
+    seq1,
+    id="1",
+    name="unk",
+    description="fsefsd"
+
+)
+
+
+record.annotations["gene"]="gene"
+record.annotations["molecule_type"]="DNA"
+
+seqf=SeqFeature(FeatureLocation(0,21),type="gene",qualifiers={"gene":"exmaple gene"})
+
+record.annotations["function"]="Simple"
+print({record.id})
+print(record)

package/6.py

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+from Bio import Seq,SeqIO,Entrez
+
+Entrez.email="heman@gmail.com"
+
+id="NM_001301717"
+
+handle =Entrez.efetch(db="nucleotide",rettype="gb",retmode="text",id=id)
+
+seqr=SeqIO.read(handle,"genbank")
+
+print(seqr)

package/7.py

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+from Bio.Align import PairwiseAligner
+from Bio.Seq import Seq
+seq1=Seq("AGTCTAGCT")
+seq2=Seq("AGCTCGTACG")
+#aligner=PairwiseAligner()
+al=PairwiseAligner().align(seq1, seq2)
+
+print(al[0])
+print(al[0].score)

package/81.py

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+from Bio.Align.Applications import MuscleCommandline
+from Bio import AlignIO
+seq1 = """>seq1
+AGTCATGCAT
+"""
+seq2 = """>seq2
+ATGCATGCAT
+"""
+seq3=""">seq3
+ACGTCGATCG
+"""
+with open("f8.fasta","w") as f:
+    f.write(seq1)
+    f.write(seq2)
+    f.write(seq3)
+
+muscle="muscle3.8.31_i86win32.exe"
+
+m_cline=MuscleCommandline(cmd=muscle,input="f8.fasta",out="aligned.fasta")
+
+stdout,stderr=m_cline()
+
+if(stderr):
+    print(stderr)
+
+
+align=AlignIO.read("aligned.fasta","fasta")
+print(align)

package/91.py

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+from Bio.Phylo.TreeConstruction import DistanceTreeConstructor ,DistanceCalculator 
+
+from Bio import Phylo ,AlignIO
+alignment=AlignIO.read("aligned_sequences.aln","clustal")
+
+cal=DistanceCalculator('identity')
+
+matrix=cal.get_distance(alignment)
+
+trees=DistanceTreeConstructor()
+tree=trees.upgma(matrix)
+
+Phylo.draw(tree)
+

package/aligned.fasta

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+>seq1
+AGTCATGCAT--
+>seq2
+ATGCATGCAT--
+>seq3
+--ACGTCGATCG

package/aligned_sequences.aln

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+CLUSTAL W(1.82) multiple sequence alignment
+
+
+seq1        ATGCGTACGTAGCTAGCTAGCTAGCTAGCTACG
+seq2        ATGCGTACGTAGCTAGCTAGCTAGCTAGCTGCG
+seq3        ATGCGTACGTAGCTAGCTAGCTAGCTAGTTACG
+seq4        ATGCGTACGTAGCTAGCTAGCTAGCTAGCTACG

package/aligned_sequences.fasta

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+>seq1
+ATGCGTACGTA
+>seq2
+ATGCGTACGTC
+>seq3
+ATGCGTACGAG

package/f8.fasta

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+>seq1
+AGTCATGCAT
+>seq2
+ATGCATGCAT
+>seq3
+ACGTCGATCG