File size: 1,980 Bytes
34393ef | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 | from Bio import SeqIO
import pandas as pd
import numpy as np
# from BCBio import GFF
import pandas as pd
import requests, sys
def fetch_seq(start, end, chr, strand):
server = "https://rest.ensembl.org"
ext = "/sequence/region/human/" + str(chr) + ":" + str(start) + ".." + str(end) + ":" + str(strand) + "?"
r = requests.get(server+ext, headers={ "Content-Type" : "text/plain"})
if not r.ok:
r.raise_for_status()
sys.exit()
return r.text
def parse_biomart(path = 'martquery_0721120207_840.txt'):
file = path
fasta_sequences = SeqIO.parse(open(file),'fasta')
genes = []
ustarts = []
uends = []
seqs = []
strands = []
tsss = []
chromosomes = []
counter = 0
for fasta in fasta_sequences:
name, sequence = fasta.id, str(fasta.seq)
if sequence != "Sequenceunavailable":
counter += 1
listed = name.split('|')
# print(len(listed))
if len(listed) == 8:
genes.append(listed[1])
chromosomes.append(listed[2])
if ';' in listed[3]:
ustart = listed[3].split(';')[0]
uend = listed[4].split(';')[0]
else:
ustart = listed[3]
uend = listed[4]
strand = int(listed[0])
if strand == -1:
ustarts.append(ustart)
uends.append(uend)
else:
ustarts.append(uend)
uends.append(ustart)
strands.append(str(strand))
tsss.append(listed[-1])
seqs.append(sequence)
# break
# print(len(seqs))
df = pd.DataFrame({'utr':seqs,'gene':genes, 'chr': chromosomes,'utr_start':ustarts,'utr_end':uends,'tss':tsss,'strand':strands})
return df
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