def directStringSeq():
my_string = "GCTGTTATGGGTCGTTGGAAGGGTGGTCGTGCTGCTGGTTAG"
Compl = complement(my_string)
reCompl = reverse_complement(my_string)
transc = transcribe(my_string)
bTransc = back_transcribe(my_string)
transl = translate(my_string)
print('my_string = ', my_string)
print('Compl = ', Compl)
print('reCompl = ', reCompl)
print('transc = ', transc)
print('bTransc = ', bTransc)
print('transl = ', transl)
def get_gc_coverage(fasta, binwidth, output):
half_width = (binwidth-1)//2
fasta_dict = {record.id:record.seq for record in SeqIO.parse(fasta, "fasta")}
header = [(chrom, len(seq)) for chrom, seq in fasta_dict.items()]
with pybw.open(output, 'w') as outbw:
outbw.addHeader(header)
for chrom, sequence in fasta_dict.items():
#pad the ends of the chromosome with mirrored sequence
padded = complement(reverse_complement(sequence[0:half_width])) + sequence + complement(reverse_complement(sequence[-half_width::]))
#should really vectorize this
gc_vector = np.zeros(len(sequence))
for i in range(len(sequence)):
gc_vector[i] = GC(padded[i:i+binwidth])
outbw.addEntries(chrom, 0, values=gc_vector, span=1, step=1)
def drawnucleotides(self):
self.calculatefontsize()
if self.display_sequence:
sequence = self.genome_window.genome.seq[
self.genome_window.
window_left:self.genome_window.window_right + 1]
if not self.genome_window.top_positive:
sequence = sequence.reverse_complement()
for x, nt, nt_comp in zip(self.genome_window.x_array, sequence,
complement(sequence)):
text = self.ax.text(x,
0,
nt,
ha='center',
va='bottom',
fontsize=self.fontsize - self.font_spacer,
color=self.color_dictionary[nt],
**self.font_kwargs)
def add_nucl(S_1, S_2, p_number_seq, count_nucl):
"""
Adds nucleotides until the linking happens
:param S_1: the first sequence
:param S_2: the second sequence
:param p_number_seq: the probability that nucleotides attach to the first strand
:param count_nucl: the number of nucleotides that enough for linkage
:return: linked sequence
"""
version_for_1 = {}
version_for_2 = {}
for i in range(len(S_1) - count_nucl + 1):
version_for_1.setdefault(S_1[i:(i + count_nucl)], []).append(i)
version_for_2.setdefault(S_2[i:(i + count_nucl)],
[]).append(len(S_1) - i - count_nucl)
while (complement(S_1[-count_nucl:]) not in version_for_2) and (complement(
S_2[:count_nucl]) not in version_for_1):
if random() < p_number_seq:
S_1 = S_1 + choices(['A', 'C', 'T', 'G'],
weights=[A_weig, C_weig, T_weig, G_weig])[0]
version_for_1.setdefault(S_1[-count_nucl:],
[]).append(len(S_1) - count_nucl)
else:
S_2 = choices(['A', 'C', 'T', 'G'],
weights=[A_weig, C_weig, T_weig, G_weig])[0] + S_2
version_for_2.setdefault(S_2[:count_nucl],
[]).append(len(S_2) - count_nucl)
if complement(S_1[-count_nucl:]) in version_for_2:
index = choice(version_for_2.get(complement(S_1[-count_nucl:])))
S = S_1 + complement(S_2[(-index - 1):])
else:
index = choice(version_for_1.get(complement(S_2[:count_nucl])))
S = S_1[:index] + complement(S_2)
return S
def molecular_weight(
seq, seq_type="DNA", double_stranded=False, circular=False, monoisotopic=False
):
"""Calculate the molecular mass of DNA, RNA or protein sequences as float.
Only unambiguous letters are allowed. Nucleotide sequences are assumed to
have a 5' phosphate.
Arguments:
- seq: String or Biopython sequence object.
- seq_type: The default is to assume DNA; override this with a string
"DNA", "RNA", or "protein".
- double_stranded: Calculate the mass for the double stranded molecule?
- circular: Is the molecule circular (has no ends)?
- monoisotopic: Use the monoisotopic mass tables?
>>> print("%0.2f" % molecular_weight("AGC"))
949.61
>>> print("%0.2f" % molecular_weight(Seq("AGC")))
949.61
However, it is better to be explicit - for example with strings:
>>> print("%0.2f" % molecular_weight("AGC", "DNA"))
949.61
>>> print("%0.2f" % molecular_weight("AGC", "RNA"))
997.61
>>> print("%0.2f" % molecular_weight("AGC", "protein"))
249.29
"""
# Rewritten by Markus Piotrowski, 2014
seq = "".join(str(seq).split()).upper() # Do the minimum formatting
if seq_type == "DNA":
if monoisotopic:
weight_table = IUPACData.monoisotopic_unambiguous_dna_weights
else:
weight_table = IUPACData.unambiguous_dna_weights
elif seq_type == "RNA":
if monoisotopic:
weight_table = IUPACData.monoisotopic_unambiguous_rna_weights
else:
weight_table = IUPACData.unambiguous_rna_weights
elif seq_type == "protein":
if monoisotopic:
weight_table = IUPACData.monoisotopic_protein_weights
else:
weight_table = IUPACData.protein_weights
else:
raise ValueError("Allowed seq_types are DNA, RNA or protein, not %r" % seq_type)
if monoisotopic:
water = 18.010565
else:
water = 18.0153
try:
weight = sum(weight_table[x] for x in seq) - (len(seq) - 1) * water
if circular:
weight -= water
except KeyError as e:
raise ValueError(
"%s is not a valid unambiguous letter for %s" % (e, seq_type)
) from None
if double_stranded:
if seq_type == "protein":
raise ValueError("protein sequences cannot be double-stranded")
elif seq_type == "DNA":
seq = complement(seq, inplace=False) # TODO: remove inplace=False
elif seq_type == "RNA":
seq = complement_rna(seq)
weight += sum(weight_table[x] for x in seq) - (len(seq) - 1) * water
if circular:
weight -= water
return weight