def gc_genes(genomes_dict_by_type_and_gen_gc3s):
gc123_by_type_and_gene_list_todas = defaultdict(dict)
for virus_genus in genomes_dict_by_type_and_gen_gc3s.keys():
for virus_type in genomes_dict_by_type_and_gen_gc3s[virus_genus]:
medias_by_gene = {}
desv_by_gene = {}
available_genes = genomes_dict_by_type_and_gen_gc3s[virus_genus][
virus_type].keys()
gc123_by_gen_dict = defaultdict(list)
for gene in available_genes:
for sequence in genomes_dict_by_type_and_gen_gc3s[virus_genus][
virus_type][gene]:
gc123 = list(GC123(sequence))
gc12 = np.mean([gc123[1], gc123[2]])
gc123.append(gc12)
gc123_by_gen_dict[gene].append(gc123)
gc123_by_gen_gc3s_array = np.asarray(gc123_by_gen_dict[gene])
gc123_by_type_and_gene_list_todas[virus_genus][
virus_type] = gc123_by_gen_dict
def mainloop():
seq = input("Sequence 1:")
seq2 = input("Sequence 2:")
alignments = pairwise2.align.globalxx(seq, seq2)
print(format_alignment(*alignments[0]))
print("No1.Total GC content:")
print(GC(seq))
print("No1.GC by parts:")
print(GC123(seq))
print("No2.Total GC content:")
print(GC(seq2))
print("No2.GC by parts:")
print(GC123(seq2))
input('next prot')
cls = lambda: os.system('cls')
cls()
mainloop()
def codon_counter(nt, codons, nt_type='dna'):
# Stores codons used for each amino acid and frequency used for said amino acid
codon_table = dict()
# Grabs the key (aa) for the given value (codon)
def get_key(val):
for key, value in codons.items():
if val in value:
return key
# Handles a RNA string passed to the codon counter
if nt_type == 'rna' and type(nt) is not Seq:
nt = Seq(nt)
nt = nt.back_transcribe()
elif nt_type == 'rna' and type(nt) is Seq:
nt = nt.back_transcribe()
start = None
stop = None
# Start and stop codons identified for the sequence
for frame in range(0, len(nt), 3):
if nt[frame:frame + 3] == 'ATG' and not start:
print(
f'Start codon {nt[frame: frame + 3]} identified at position {frame}'
)
start = frame
# mRNA-1273 contains all three stop codons at the end of the sequence
# TAG was the last one before the 3' UTR so all stop codons included in the codon table
if nt[frame:frame + 3] == 'TAG' and not stop:
print(
f'Stop codon {nt[frame: frame + 3]} identified at position {frame}'
)
stop = frame + 3
# Trimmed nt sequence starting at ATG and ending at TAG
nt_cds = nt[start:stop]
prev_codon = ''
# Counting codons used per amino acid
for frame in range(3, (len(nt_cds) + 3), 3):
aa = get_key(nt_cds[frame - 3:frame])
codon_table.setdefault(aa, []).append(str(nt_cds[frame - 3:frame]))
# Returns a list of tuples (codon, num times used to translate aa in nt seq provided / total codons for aa)
for aa in codon_table.keys():
codon_counts = {
aa: [(codon,
round(codon_table[aa].count(codon) / len(codon_table[aa]),
3)) for codon in set(codon_table[aa])]
}
codon_table.update(codon_counts)
print(GC123(nt_cds))
return codon_table
def calculate_GC(entries):
gc, gc1, gc2, gc3 = [], [], [], []
name, sequences = list(zip(*entries))
for seq in sequences:
_gc, _gc1, _gc2, _gc3 = GC123(seq)
gc.append(_gc)
gc1.append(_gc1)
gc2.append(_gc2)
gc3.append(_gc3)
df = pd.DataFrame([[x / 100.0 for x in gc], [x / 100.0 for x in gc1],
[x / 100.0 for x in gc2], [x / 100.0 for x in gc3]]).T
df.columns = "gc_content gc1_content gc2_content gc3_content".split()
return df
def calculate123(seq_path):
result_df = pd.DataFrame(
columns=["seqid", "GC", "GC12", "GC1", "GC2", "GC3"])
seq_list = SeqIO.parse(seq_path, "fasta")
for record in seq_list:
tmp_dict = dict()
tmp_dict["seqid"] = record.id
tmp_dict["GC"], tmp_dict["GC1"], tmp_dict["GC2"], tmp_dict[
"GC3"] = GC123(record.seq)
tmp_dict["GC12"] = (tmp_dict["GC1"] + tmp_dict["GC2"]) / 2
result_df = result_df.append(tmp_dict, sort=False, ignore_index=True)
result_df.iloc[:, 1:] = result_df.iloc[:, 1:] / 100
return result_df
def gc_length(input_file, output, field=None, header=None):
"""
Given an input tab-delimited field, retrieve sequences at the given field
(default = last field of tab-delimited file) computes GC content and length
and outputs file. Header specifies if input has header
"""
gapped = Gapped(ExtendedIUPACDNA(), '-') # Extend alphabet to allow gaps
if field is None:
field = -1
if header is None:
header = True
with open(input_file, "r") as in_file:
sequences = []
number = 0
for line in in_file:
if not header:
line = line.split("\t")
sequences.append(Seq(line[field], gapped))
if header and number > 0:
line = line.split("\t")
sequences.append(Seq(line[field], gapped))
number += 1
with open(output, "w") as o_file:
dinuc_list = ["".join(x) for x in product("ATCG", repeat=2)]
header = "AoverAT\tGCm\tlength"
for nuc in "ATCG":
header += "\t{}.freq".format(nuc)
for dinuc in dinuc_list:
header += "\t{}.freq".format(dinuc)
header += "\tSeq"
print(header, file=o_file)
for seq in sequences:
gc = GC123(seq)
at = AoverAT(seq)
nuc_freq = nucleotide(seq)
dinuc_freq = dinucleotide(seq)
line = "{}\t{}\t{}".format(at, gc[0], len(seq)-1)
for nuc in "ATCG":
line += "\t{}".format(float(nuc_freq[nuc]))
for dinuc in dinuc_list:
line += "\t{}".format(float(dinuc_freq[dinuc]))
line += "\t{}".format(seq.tostring())
line = line.rstrip("\n")
print(line, file=o_file)
def GC3(sequ):
"""Calculates the GC content an the 3rd codon position..
Args:
sequ (str): DNA sequence
Returns:
int: GC3 value
"""
from Bio.SeqUtils import GC123
GC3 = round(GC123(sequ)[3], 3)
return GC3
def gc123(fasta, output=()):
#create header
a = [['Transcript', 'GC', 'GC1', 'GC2', 'GC3']]
#parse and read over fasta file
for b in SeqIO.parse(open(fasta, "r"), "fasta"):
#use Biopython GC123 to calculate GC content and codon GC content
c = GC123(b.seq)
#for each sequence, add these values to the array
a = a + [[b.id, str(c[0]), str(c[1]), str(c[2]), str(c[3])]]
#output results
if output:
with open(output, 'w') as d:
d.writelines('\t'.join(e) + '\n' for e in a)
else:
return (a)
def biodb2cds_gc(biodb):
from chlamdb.biosqldb import manipulate_biosqldb
from Bio.SeqUtils import GC123
server, db = manipulate_biosqldb.load_db(biodb)
sql1 = 'select distinct accession from orthology_detail_%s' % biodb
sql2 = 'select locus_tag, taxon_id from orthology_detail_%s' % biodb
sql3 = 'select locus_tag, seqfeature_id from custom_tables.locus2seqfeature_id_%s' % biodb
accession_list = [i[0] for i in server.adaptor.execute_and_fetchall(sql1,)]
locus2taxon_id = manipulate_biosqldb.to_dict(server.adaptor.execute_and_fetchall(sql2,))
locus2seqfeature_id = manipulate_biosqldb.to_dict(server.adaptor.execute_and_fetchall(sql3,))
sql_head = 'create table IF NOT EXISTS custom_tables.gc_content_%s (taxon_id INT, ' \
' seqfeature_id INT,' \
' seq_length INT, gc_percent FLOAT, gc_1 FLOAT, gc_2 FLOAT, gc_3 FLOAT, ' \
' INDEX seqfeature_id(seqfeature_id), index taxon_id(taxon_id))' % biodb
server.adaptor.execute(sql_head,)
count_all=0
for accession in accession_list:
print (accession)
record = db.lookup(accession=accession)
seq = record.seq
for n, feature in enumerate(record.features):
if feature.type == 'CDS' and not 'pseudo' in feature.qualifiers and not 'pseudogene' in feature.qualifiers and 'translation' in feature.qualifiers:
count_all+=1
dna_sequence = feature.extract(seq)
locus = feature.qualifiers['locus_tag'][0]
gc, gc1, gc2, gc3 = GC123(str(dna_sequence))
sql = 'insert into custom_tables.gc_content_%s values (%s, %s, %s, %s, %s, %s, %s);' % (biodb,
locus2taxon_id[locus],
locus2seqfeature_id[locus],
len(dna_sequence),
round(gc,2),
round(gc1),
round(gc2),
round(gc3))
server.adaptor.execute(sql,)
server.commit()
def get_gene_gc_len(genes_d):
''' Return list of gene GC and GC3, gene sizes, and detailed gene informations'''
gcs = []
gc3s = []
lens = []
info = []
for scfid, l in genes_d.iteritems():
for geneid, gene_start, gene_end, strand, description, gene_seq in l:
gc = GC(gene_seq)
gc3 = GC123(gene_seq)[3]
length = len(gene_seq)
gcs.append(gc)
gc3s.append(gc3)
lens.append(length)
info.append([
scfid, geneid, strand, length, gc, gc3, gene_start, gene_end,
strand, description
])
return gcs, gc3s, lens, info
def calculate123(seq_path):
seq_list = SeqIO.parse(seq_path, "fasta")
dict_list = []
for record in seq_list:
tmp_dict = dict()
tmp_dict["GC"], tmp_dict["GC1"], tmp_dict["GC2"], tmp_dict[
"GC3"] = GC123(record.seq) / 100
tmp_dict['slen'] = len(record.seq)
dict_list.append(tmp_dict)
result_df = pd.DataFrame(dict_list)
result_dict = {
'seqid': splt(seq_path)[1],
'GC': sum(result_df.GC * result_df.slen) / result_df.slen.sum() / 100,
'GC1':
sum(result_df.GC1 * result_df.slen) / result_df.slen.sum() / 100,
'GC2':
sum(result_df.GC2 * result_df.slen) / result_df.slen.sum() / 100,
'GC3': sum(result_df.GC3 * result_df.slen) / result_df.slen.sum() / 100
}
return result_dict
def gc123_genomes(genomes_dict):
gc123_output_list = defaultdict(dict)
for virus_genus in genomes_dict.keys():
for virus_type in genomes_dict[virus_genus].keys():
gc123_values = []
for record in genomes_dict[virus_genus][virus_type]:
gc123 = list(GC123(record.seq))
gc12 = np.mean([gc123[1], gc123[2]])
gc123.append(gc12)
gc123_values.append(gc123)
gc123_output_list[virus_genus][virus_type] = gc123_values
return gc123_output_list
from Bio.SeqUtils import GC
from Bio.SeqUtils import GC123
seq = input(str("DNA manual:"))
print("Total GC content:")
print(GC(seq))
print("GC by parts:")
print(GC123(seq))
input("enter")
# --------------------------------------------
'''
print(step3)
levelTwoType = []
geneDist = os.path.join(outdir, "gene.dist.tsv")
with open(geneDist, 'w') as f:
f.write("id\ttranscript_num\tgc\tgc1\tgc2\tgc3\tlength\n")
for gene in db.features_of_type("gene"):
transcriptCounts = str(len(list(db.children(gene))))
transcriptType = [t.featuretype for t in db.children(gene, level=1)]
levelTwoType += transcriptType
geneFa = gene.sequence(fasta)
gc = GC(geneFa)
gc123 = GC123(geneFa)
geneLen = gene.end - gene.start + 1
items = [
gene.id, transcriptCounts,
str(gc),
str(gc123[1]),
str(gc123[2]),
str(gc123[3]),
str(geneLen)
]
linestr = '\t'.join(items)
f.write(linestr + '\n')
print(set(levelTwoType))
# 基因间区长度分布
def parsing_genom_CDS():
chain = ""
liste_gen = parsing_fasta("tmp.txt.genome")
if liste_gen:
##recuperer les TaxID
with open('tmp.txt') as f:
line = f.readline()
line = line.rstrip()
line = int(float(line))
len_gen = 0
N = 0
gc = 0
for i in liste_gen:
len_gen = len_gen + len(str(i)) #lengueur des chromosomes
for j in str(i):
if j == 'N':
N = N + 1 #nbr de N dans la seq génomique
if j in ['G', 'C']:
gc = gc + 1
len_gen_valid = len_gen - N
gc = gc * 100 / float(len_gen_valid) #taux de GC genome
N = N / float(len_gen) #%NA
#print(gc, N, len_gen, len_gen_valid)
####CDS
li = parsing_fasta("tmp.txt.cds")
if li:
lis = []
a = 0 #taux GC CDSvalid
b = 0 #taux GC1 CDSvalid
c = 0 #taux GC2 CDSvalid
d = 0 #taux GC3 CDSvalid
LenCumCDS = 0
NbrCDS_valid = 0
LenCumCDS_valid = 0
j = 0
#NbrCDS = len(li)
for i in li:
i = str(i)
j = j + 1
LenCumCDS = LenCumCDS + len(i)
if CDS_Conformity(i):
NbrCDS_valid += 1
LenCumCDS_valid += len(i)
lis = GC123(i)
a += lis[0]
b += lis[1]
c += lis[2]
d += lis[3]
else:
pass
NbrCDS = j
#print(j, NbrCDS_valid, LenCumCDS, LenCumCDS_valid)
#print(a/len(li),b/len(li),c/len(li),d/len(li))
lst = [
line, len_gen,
round(gc),
round(N), NbrCDS, LenCumCDS,
round(a / len(li)), NbrCDS_valid, LenCumCDS_valid,
round(b / len(li)),
round(c / len(li)),
round(d / len(li))
]
lst = map(str, lst)
chain = "\t".join(lst)
chain = chain + '\n'
return chain
def parsing_genom_CDS():
##recuperer les TaxID
with open('tmp.txt') as f:
line = f.readline()
line = line.rstrip()
line = int (float(line))
#construire fichier CSV pour stocker les résultats
#res = csv.writer(open("resultats.csv", "wb"))
#c.writerow(["TaxId","LenGenome","GCgenome","%NA","NbrCDS","LenCumCDS","GC_CDS","NbrCDS_valid","LenCumCDS_valid","GC1","GC2","GC3"])
liste_gen = parsing_fasta("tmp.txt.genome")
len_gen = 0
N = 0
gc = 0
for i in liste_gen:
len_gen = len_gen + len(str(i)) #lengueur des chromosomes
for j in str(i):
if j == 'N':
N = N + 1 #nbr de N dans la seq génomique
if j in ['G', 'C']:
gc = gc + 1
len_gen_valid = len_gen - N
gc = gc*100/float(len_gen_valid) #taux de GC genome
N = N / float(len_gen) #%NA
#print(gc, N, len_gen, len_gen_valid)
####CDS
li = parsing_fasta("tmp.txt.cds")
lis = []
a = 0
b = 0
c = 0
d = 0
LenCumCDS = 0
NbrCDS_valid = 0
LenCumCDS_valid = 0
j = 0
#NbrCDS = len(li)
for i in li:
i = str(i)
j = j +1
LenCumCDS = LenCumCDS + len(i)
if CDS_Conformity(i):
NbrCDS_valid += 1
LenCumCDS_valid +=len(i)
lis = GC123(i)
a +=lis[0]
b +=lis[1]
c +=lis[2]
d +=lis[3]
else:
pass
NbrCDS = j
#print(j, NbrCDS_valid, LenCumCDS, LenCumCDS_valid)
#print(a/len(li),b/len(li),c/len(li),d/len(li))
lst = [line, len_gen, round(gc), round(N), NbrCDS, LenCumCDS, round(a/len(li)), NbrCDS_valid, LenCumCDS_valid, round(b/len(li)), round(c/len(li)), round(d/len(li))]
lst = map(str, lst)
chain = "\t".join(lst)
chain = chain + '\n'
return chain
# print( brin1[1:] )
# print( brin1[1:].translate() )
# print( brin1[2:] )
# print( brin1[2:].translate() )
## known bug for six_frame_translations !!
from Bio.SeqUtils import six_frame_translations
print( "" )
# print(six_frame_translations( fasta_seq_toTest ) )
# print(six_frame_translations( genba_seq_toTest ) )
## does not work above for GC()
from Bio.SeqUtils import GC, GC123
print( "" )
# print(GC( fasta_seq_toTest ) )
print(GC123( fasta_seq_toTest ) )
# print(GC( genba_seq_toTest ) )
print(GC123( genba_seq_toTest ) )
## NCBI connection
def FetchSeq(mydb, myrettype, myretmode, myid):
from Bio import Entrez
from Bio import SeqIO
Entrez.email = "*****@*****.**"
with Entrez.efetch(db=mydb, rettype=myrettype, retmode=myretmode, id=myid) as handle:
seq_record = SeqIO.read(handle, "fasta")
print("%s with %i features" % (seq_record.id, len(seq_record.features)))
print( "***** FetchSeq nucleotide fasta text 6273291" )
FetchSeq("nucleotide", "fasta", "text", "6273291")
from Bio import SeqIO
fasta_file = "capybara_genes.fasta" # Input fasta file
gene_code = ['Capybara_gene_code']
gc_content_tot = ['GC_content_total']
gc_first = ['GC_first_codon_pos']
gc_second = ['GC_second_codon_pos']
gc_third = ['GC_third_codon_pos']
gene_length = ['Gene_length']
protein_length = ['Prot_length']
fasta_sequences = SeqIO.parse(open(fasta_file), 'fasta')
for seq in fasta_sequences:
gene_code.append(seq.id) #ID exists only for 'Record' objects
gc_content_tot.append(GC123(seq)[0])
gc_first.append(GC123(seq)[1])
gc_second.append(GC123(seq)[2])
gc_third.append(GC123(seq)[3])
gene_length.append(len(seq))
protein_length.append(len(seq) / 3)
gene_code = np.array(gene_code)
gc_content_tot = np.array(gc_content_tot)
gc_first = np.array(gc_first)
gc_second = np.array(gc_second)
gc_third = np.array(gc_third)
gene_length = np.array(gene_length)
protein_length = np.array(protein_length)
tbl = np.column_stack((gene_code, gc_content_tot, gc_first, gc_second,
gc_third, gene_length, protein_length))
fastaArray = []
id_Fasta = ''
for i in range(0,
len(fastaLines) -
1): #from 0 to the number of lines in the file minus one
lines = fastaLines[i]
if lines.startswith('>'):
id_Fasta = lines.strip(
'>') #strip removes leading and trailing characters
id_Fasta = id_Fasta.strip(
'\n') #strip removes leading and trailing characters
id_Fasta = id_Fasta.strip(
'\s') #strip removes leading and trailing characters
count = resultArray.index(id_Fasta)
fastaLines[i + 1] = fastaLines[i + 1].strip('\n')
gc_1 = round(GC123(fastaLines[i + 1])[1], 2)
gc_2 = round(GC123(fastaLines[i + 1])[2], 2)
gc_3 = round(GC123(fastaLines[i + 1])[3], 2)
gc_overall = round(GC(fastaLines[i + 1]), 2)
outputFile.write('>' + resultLineArray[count] + '\t' + str(gc_1) +
'\t' + str(gc_2) + '\t' + str(gc_3) + '\t' +
str(gc_overall) + '\n')
outputFile.write(fastaLines[i + 1] + '\n')
resultArray.pop(count)
resultLineArray.pop(count)
outputFile.close()
#!/usr/bin/python
# testing python script
import Bio as bio
import matplotlib.pyplot as plot
from Bio.Seq import Seq
from Bio.Alphabet import generic_rna,generic_dna
from Bio.SeqUtils import GC123,GC,GC_skew
seq = "ataccaggctgaggcccattaatgatgcaatttgctgggcttctctattttctccgtgcttccatcctcttctccgtcggcggggagaagtgaaatgccgtggagatgggcggcggcggcggcgacggcggcgacgagaaagctcaccgggatctctcagtcgcgagtttcagtagcctttaccggccgtcttctctaccgctcgttcggaagcgactccagtgaaagccgcaagaggtcactgccacggggggtcgtatcgatcggggccatcagccttgctggaggtctcgtgctcagcgccgtcaacgacctcgccatcttcaatggatgcacaacgaaggcaattgagcatgctgctgacaaccctgctgttgtggaagcaattggagtgcctatagtcagaggaccgtggtatgatgcttctcttgaggtgggccatcgacggcggtctgtgtcatgcacattccctgtatctgggccacatgggtcaggatttctccagattaaggcaacccgagatggagaggatggtctgctttcgtttctgcggcatcacgactggaagatcctattgctggaggctcatcttgaagcaccatcagatgatgaggaccagagaaagctggttaaggtgaatcttgcaagcagtggccgtggggaagatggggatccagagagtggttaatcttttgtactgaattccatggtgagtggaagatcgtgtcatctgaatggactccaaatattaaatgacatggagatctagggaagcaaaaaaaaaaaaaaaa"
print GC123(seq)
print GC(seq)
plot(GC_skew(seq,window=100),c="r")
xlabel("Window")
ylabel("(G-C)/(G+C)")
title("GC-skew")
