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filter.py
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filter.py
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import requests
from bs4 import BeautifulSoup
from blast import read_blast
def filter_summary(results: list, filter: str) -> list:
"""
Filter the results of a summary file based on a taxonomic filter. Any
species that belongs to that filter will be included in the returned list.
The original results list is not modified.
:param results: A list of strings containing the results of a BLAST search.
:param filter: The name of the taxon to filter by.
"""
# Loop through each line in the results and check the species lineage.
removed = 0
filter_upper = filter.upper()
# Get tuples of where each entry starts and ends
entries = []
start = False
lineage = None
i1 = -1
for i in range(len(results)):
if start:
if (not (results[i].startswith('\t') or
results[i][0] == '-' or
results[i].startswith('Lineage: '))) or (i == len(results) - 1):
i2 = i
entries.append((i1, i2, filter_upper in lineage))
start = False
if not (results[i].startswith('\t') or results[i][0] == '-' or
results[i].startswith('Lineage: ')):
start = True
i1 = i
if results[i].startswith('Lineage: '):
lineage = results[i].split('Lineage: ')[1]
lineage = lineage.split(';')
lineage = [x.strip().upper() for x in lineage]
# Remove entries that are not in the filter lineage
res = []
for entry in entries:
if not entry[2]:
removed += 1
else:
res += results[entry[0]:entry[1]]
res.insert(0, f'Removed {removed} results not in lineage {filter}\n\n')
return res
def filter_blast(blast_file: str, filter: str) -> list:
"""
Filter the blast output based on a taxonomic filter.
:param blast_file: The path to the BLAST file.
:param filter: The name of the taxon to filter by.
"""
# Read the results
results = read_blast(blast_file)
# Get the taxids
ids = [results[x]['taxid'] for x in results]
# Make sure the ids are unique
ids = list(set(ids))
# Send the request
url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?" \
"db=taxonomy&id={IDS}"
r = requests.get(url.format(IDS=",".join(ids)))
# Map the IDs to their respective lineages
tax_map = _map_id_to_lineage(r)
# Filter the results
filtered = []
for result in results:
taxid = results[result]['taxid']
lineage = tax_map[taxid]
if filter in lineage:
filtered.append(result)
return filtered
def _map_id_to_lineage(r: requests.Response) -> dict:
"""
Given the response from the NCBI taxonomy database, map the IDs to their
respective lineages.
:param r: The response from the NCBI taxonomy database.
"""
# Parse the XML results using BeautifulSoup
soup = BeautifulSoup(r.text, features='xml')
# Remove all of 'LineageEx'
for x in soup.find_all('LineageEx'):
x.decompose()
# Get taxids and lineages
taxa = soup.findAll('Taxon')
# Build the map of tax ID to lineage
tax_map = {}
for taxon in taxa:
tax_map[taxon.TaxId.text] = taxon.Lineage.text.split('; ')
return tax_map