biopyhton programs

# GC percentage
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
from Bio.SeqUtils import GC
my_seq = Seq(input("Plak DNA sequentie"), IUPAC.unambiguous_dna)
print(GC(my_seq))

#Print lengte en nummering
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC

my_seq = Seq(input("Plak de sequentie"), IUPAC.unambiguous_dna)
for index, letter in enumerate(my_seq):
    print("%i %s" % (index, letter))
print(len(my_seq)) # print de totale lengte van de sequentie
print(my_seq[10]) # print een exacte aangegeven element uit


# Gen silencen
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC

my_seq = Seq("GATCGATGGGCCTATATAGGATCGAAAATCGC", IUPAC.unambiguous_dna)
print(my_seq[2:12])


#Toevoegen van sequenties
from Bio.Seq import Seq
from Bio.Alphabet import generic_nucleotide
from Bio.Alphabet import IUPAC

nuc_seq = Seq(input(" plak Sequentie 1"), generic_nucleotide)
dna_seq = Seq(input("Plak Sequentie 2"), IUPAC.unambiguous_dna)

print(nuc_seq + dna_seq)

#Meerdere sequenties (werkt niet)
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna

list_of_seqs = [Seq("ACGT", generic_dna), Seq("AACC", generic_dna), Seq("GGTT", generic_dna)]
sum(list_of_seqs, Seq("", generic_dna))

#Veranderen van Higher/lowercase
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna

dna_seq = Seq("acgtACGT", generic_dna)
print(dna_seq.upper())
print(dna_seq.lower())

#Seqenties in (reverse) complementair
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC

my_seq = Seq("GAAAAAC", IUPAC.unambiguous_dna)
print(my_seq.complement())
print(my_seq.reverse_complement())

#DNA naar RNA (transcriptie)
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC

coding_dna = Seq("CAGTCGAGCGATTGAA", IUPAC.unambiguous_dna)
template_dna = coding_dna.reverse_complement()
print(template_dna.reverse_complement().transcribe())

#RNA naar DNA (reverse transcriptase)
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC

messenger_rna = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG", IUPAC.unambiguous_rna)
print(messenger_rna.back_transcribe())

#Translatie RNA -> eiwit
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC

messenger_rna = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG", IUPAC.unambiguous_rna)
print(messenger_rna.translate())

#Translatie DNA -> eiwit
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC

coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG", IUPAC.unambiguous_dna)
print(coding_dna.translate())

#Translatie gen
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
gene = Seq("GTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCA" + \
           "GCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGATAGGCGATCGTGAT" + \
           "AATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCTGGTGGAAACAACAT" + \
           "TATGAATGGCGAGGCAATCGCTGGCACCTACACGGACCGCCGCCACCGCCGCGCCACCAT" + \
           "AAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACATCACCGCTAA", generic_dna)
print(gene.translate(table="Bacterial"))

#Translatie tabellen (gewervelde)
from Bio.Data import CodonTable

standard_table = CodonTable.unambiguous_dna_by_name["Standard"]
mito_table = CodonTable.unambiguous_dna_by_name["Vertebrate Mitochondrial"]
print(standard_table)
print(standard_table.start_codons)

#Vergelijken van sequenties.
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC

seq1 = Seq(input("Plak DNA sequentie 1"), IUPAC.unambiguous_dna)
seq2 = Seq(input("Plak DNA sequentie 2"), IUPAC.ambiguous_dna)
print(str(seq1) == str(seq2))