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lib.py
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lib.py
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#!/usr/bin/env python
"""
Created by: Lee Bergstrand
Description: Functions for HMMER-DB.
"""
# Imports & Setup:
import csv
import sys
from Bio import SeqIO
import subprocess
import re
# Regex's
LocusRegex = re.compile("\(Locus:\s\S*\)")
LocationRegex = re.compile("\(Location:\s\[(\S*)\:(\S*)\]\((\S)\)\)")
# ----------------------------------------------------------------------------------------
def extract_sequence_records(organism_file_path, file_type):
"""
Read in sequence files as a sequence record object using Biopython.
:param organism_file_path: The path to the input file.
:return: Biopython sequence record object.
"""
try:
print(">> Opening FASTA file: " + organism_file_path)
handle = open(organism_file_path, "rU")
try:
records = list(SeqIO.parse(handle, file_type))
except ValueError as error:
print("Error has occurred while parsing " + organism_file_path + "!")
print(str(error))
sys.exit(1)
handle.close()
except IOError:
print("Failed to open " + organism_file_path)
sys.exit(1)
return records
# -----------------------------------------------------------------------------------------------------------
def check_extensions(organism_file_path, csv_file_path, hmm_file_paths, sql_file_paths):
"""
Performs file extension checks.
:param organism_file_path: Path to the organism database file.
:param csv_file_path: Path to the organism information database file.
:param hmm_file_paths: Path to the HMM model file.
:param sql_file_paths: Path to the sqlite3 file.
"""
print(">> Performing file extension checks...")
if not organism_file_path.endswith(".faa"):
print("[Warning] " + organism_file_path + " may not be a fasta file!")
if not csv_file_path.endswith(".csv"):
print("[Warning] " + csv_file_path + " may not be a csv file!")
for hmm_path in hmm_file_paths:
if not hmm_path.endswith(".hmm"):
print("[Warning] " + hmm_path + " may not be a HMM file!")
if not sql_file_paths.endswith(".sqlite"):
print("[Warning] " + sql_file_paths + " may not be a sqlite file!")
# ----------------------------------------------------------------------------------------
def generate_fasta_string(sec_record_list):
"""
Creates a FASTA formatted string containing sequences from a list of sequence record objects.
:param sec_record_list: List of Biopython sequence record objects.
:return: String containing FASTA formatted strings.
"""
fasta_string_list = []
for record in sec_record_list:
fasta_string_list.append(record.format("fasta"))
fasta_string = ''.join(fasta_string_list)
return fasta_string
# ----------------------------------------------------------------------------------------
def generate_fasta_dict(sec_record_list):
"""
Creates a dictionary containing FASTA formatted strings from a list of sequence record objects.
This dictionary is keyed by the sequence ID.
:param sec_record_list: List of Biopython sequence record objects.
:return: Dictionary containing FASTA formatted strings.
"""
fasta_string_dict = {}
for record in sec_record_list:
fasta_string_dict[record.id] = record.format("fasta")
return fasta_string_dict
# ----------------------------------------------------------------------------------------
def hmm_search(fasta_string, hmmer_model_path, processes):
"""
Runs HMMER with settings specific for extracting subject sequences.
:param fasta_string: String containing protein sequences in FASTA format.
:param hmmer_model_path: Path to the HMM model to be used as a query.
:return: String containing hmmsearch output.
"""
process = subprocess.Popen(["hmmsearch", "--acc", "--cpu", str(processes), hmmer_model_path, "-"],
stdin=subprocess.PIPE, stdout=subprocess.PIPE, bufsize=1)
# This returns a list with both stderr and stdout. Only return stdout. Fail if error.
stdout, error = process.communicate(fasta_string)
if error:
print(str(error))
sys.exit(1)
else:
return stdout
# ------------------------------------------------------------------------------------------------------------
def get_hit_protein_data(hmm_hit_table, annotation_fasta_dict, organism_accession):
"""
Creates a list of lists which contain protein information.
:param hmm_hit_table: Table of HMM hit objects.
:param annotation_fasta_dict: Dictionary containing FASTA sequences keyed by their IDs
:param organism_accession: The accession of the organism.
:return: A list of lists of hit protein properties.
"""
hit_proteins = []
for hit in hmm_hit_table:
protein_accession = hit.target_protein
protein_fasta = annotation_fasta_dict[protein_accession]
locus = str(LocusRegex.search(protein_fasta).group(0))
locus = locus.split()[1].rstrip(")")
location_data = LocationRegex.search(protein_fasta)
try:
start = int(location_data.group(1))
end = int(location_data.group(2))
strand = location_data.group(3)
protein_data = [protein_accession, organism_accession, locus, start, end, strand, protein_fasta]
hit_proteins.append(protein_data)
except AttributeError as error:
print(hit)
print(protein_fasta)
print(location_data)
print("This is the organism: ", organism_accession)
print("The AttributeError was ", str(error))
sys.exit(1)
return hit_proteins
# -----------------------------------------------------------------------------------------------------------
def extract_csv_dict(input_csv_path):
"""
Opens OrganismDB CSV file for reading and stores as dictionary.
:param input_csv_path: Path to the input OrganismDB CSV file.
:return: Dictionary with each row in the CSV keyed by the organism accession (CSV row one).
"""
organism_data_csv = {}
try:
print(">> Opening organism CSV file: " + input_csv_path)
read_file = open(input_csv_path, "r")
reader = csv.reader(read_file)
for row in reader:
organism_data_csv[row[0].split('.')[0]] = row # Row[0] is the organism accession.
read_file.close()
except IOError:
print("Failed to open " + input_csv_path)
sys.exit(1)
return organism_data_csv
# -----------------------------------------------------------------------------------------------------------
def insert_organism_info(db_cursor, organism_info):
"""
Inserts organism info into DB.
:param db_cursor: Sqlite3 database cursor.
:param organism_info: List containing organism info.
"""
query = '''INSERT OR REPLACE INTO Organisms
(
Organism_Accession,
Accession_Type,
Organism_Description,
Source,
Organism_Phylogeny,
Sequence_Length
)
VALUES
(?,?,?,?,?,?)'''
db_cursor.execute(query, organism_info)
# -----------------------------------------------------------------------------------------------------------
# 8:
def insert_proteins(db_cursor, hit_proteins):
"""
Inserts protein info into DB.
:param db_cursor: Sqlite3 database cursor.
:param hit_proteins: List containing protein info.
"""
query = '''INSERT OR REPLACE INTO Proteins
(
Protein_Accession,
Organism_Accession,
Locus,
Start,
"End",
Strand,
FASTA_Sequence
)
VALUES
(?,?,?,?,?,?,?)'''
for protein in hit_proteins:
db_cursor.execute(query, protein)
# -----------------------------------------------------------------------------------------------------------
def insert_hits(cursor, hmm_hit_list):
"""
Inserts hits into DB and creates md5 hash for primary key.
:param cursor: Sqlite3 database cursor.
:param hmm_hit_list: List of hmm hit objects.
"""
query = '''INSERT OR REPLACE INTO HMM_Hits
(
Hit_HASH,
Protein_Accession,
HMM_Model,
HMM_Score,
HMM_E_Value,
Ali_From,
Ali_To,
HMM_From,
HMM_To,
HMM_Coverage
)
VALUES
(?,?,?,?,?,?,?,?,?,?)'''
for hit in hmm_hit_list:
hit_list = [hit.get_md5(), hit.target_protein, hit.hmm_name, hit.score, hit.e_value, hit.ali_from, hit.ali_to,
hit.hmm_from, hit.hmm_to, hit.hmm_coverage]
cursor.execute(query, hit_list)