| from Bio import SeqIO |
| import pandas as pd |
| import numpy as np |
| |
| 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('|') |
| |
|
|
| 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) |
|
|
| |
| |
| df = pd.DataFrame({'utr':seqs,'gene':genes, 'chr': chromosomes,'utr_start':ustarts,'utr_end':uends,'tss':tsss,'strand':strands}) |
| return df |
|
|
