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populate_seqDB.py
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populate_seqDB.py
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import os
import sys
import sqlite3
from Bio import SeqIO
from collections import defaultdict
def createTables (cursor):
try:
tables_to_create = ['CREATE TABLE "Genes" ("Gene_ID" TEXT, "Transcript_IDs" TEXT NOT NULL, "Ortholog_ID" TEXT, PRIMARY KEY("Gene_ID"))',
'CREATE TABLE "Orthologs" ("Ortholog_ID" TEXT,"Transcript_IDs" TEXT NOT NULL, PRIMARY KEY("Ortholog_ID"))',
'CREATE TABLE "Protein" ("Transcript_ID" TEXT, "Sequence" BLOB NOT NULL, PRIMARY KEY("Transcript_ID") )',
'CREATE TABLE "mRNA" ("Transcript_ID" TEXT, "Sequence" BLOB NOT NULL, PRIMARY KEY("Transcript_ID") )']
for table_to_create in tables_to_create:
# Execute the insert values command
cursor.execute(table_to_create)
except sqlite3.Error as error:
raise Exception(error)
def addSequence (cursor, table, transcript_ID, fasta_sequence):
try:
# Create the insert string
sqlite_insert_values = 'INSERT INTO %s (Transcript_ID, Sequence) VALUES (?, ?)' % table
# Convert the sequence to binary
fasta_sequence = sqlite3.Binary(fasta_sequence.encode())
# Execute the insert values command
cursor.execute(sqlite_insert_values, (transcript_ID, fasta_sequence))
except sqlite3.Error as error:
raise Exception(error)
def addGene (cursor, gene_ID, transcript_IDs):
try:
# Create the insert string
sqlite_insert_values = 'INSERT INTO Genes (Gene_ID, Transcript_IDs) VALUES (?, ?)'
# Execute the insert values command
cursor.execute(sqlite_insert_values, (gene_ID, transcript_IDs))
except sqlite3.Error as error:
raise Exception(error)
def addGeneOrtho (cursor, gene_ID, transcript_IDs, ortholog_ID):
try:
# Create the insert string
sqlite_insert_values = 'INSERT INTO Genes (Gene_ID, Transcript_IDs, Ortholog_ID) VALUES (?, ?, ?)'
# Execute the insert values command
cursor.execute(sqlite_insert_values, (gene_ID, transcript_IDs, ortholog_ID))
except sqlite3.Error as error:
raise Exception(error)
def addOrtholog (cursor, ortholog_ID, transcript_IDs):
try:
# Create the insert string
sqlite_insert_values = 'INSERT INTO Orthologs (Ortholog_ID, Transcript_IDs) VALUES (?, ?)'
# Execute the insert values command
cursor.execute(sqlite_insert_values, (ortholog_ID, transcript_IDs))
except sqlite3.Error as error:
raise Exception(error)
# Connect to the sqlite database
sqlite_connection = sqlite3.connect('SequenceDB.sqlite')
# Create the cursor
cursor = sqlite_connection.cursor()
createTables(cursor)
# Create dict to store the ortholog group for a transcript
transcript_to_ortholog = {}
# Loop the files within the ortholog directory
for ortholog_file in os.listdir(sys.argv[2]):
# Assign the ortholog ID, from the filename
ortholog_ID = os.path.splitext(ortholog_file)[0].replace('og_cds_', 'OG_')
# Create list to store the orthologs
orthologous_transcript_list = []
# Read the ortholog file
for record in SeqIO.parse(os.path.join(sys.argv[2], ortholog_file), "fasta"):
# Remove if the other genomes are found
if '-R' not in record.id:
continue
# Append the ID
orthologous_transcript_list.append(record.id)
# Assign the ortholog group to the current gene
transcript_to_ortholog[record.id] = ortholog_ID
# Save the IDs as a string
orthologous_transcripts = ', '.join(orthologous_transcript_list)
# Add the ortholog
addOrtholog (cursor, ortholog_ID, orthologous_transcripts)
# Walk the Assembly directory
for root, dirs, files in os.walk(sys.argv[1]):
# Loop the Assembly files
for name in files:
if '_trans.fasta' in name:
# Create an ID dict
id_dict = defaultdict(list)
# Loop the sequence
for record in SeqIO.parse(os.path.join(root, name), "fasta"):
# Assign the gene ID
record_gene_id = record.id.split('-')[0]
# Add the gene ID and transcript ID to the dict
id_dict[record_gene_id].append(record.id)
# Open the file as an index
record_index = SeqIO.index(os.path.join(root, name), "fasta")
# Loop the dict by gene
for gene_ID, transcript_IDs in id_dict.items():
# Loop the transcripts
for transcript_ID in transcript_IDs:
# Add the sequence to the database
addSequence(cursor, 'mRNA', transcript_ID, record_index[transcript_ID].format("fasta"))
if '_pep.fasta' in name:
# Create an ID dict
id_dict = defaultdict(list)
# Loop the sequence
for record in SeqIO.parse(os.path.join(root, name), "fasta"):
# Assign the gene ID
record_gene_id = record.id.split('-')[0]
# Add the gene ID and transcript ID to the dict
id_dict[record_gene_id].append(record.id)
# Open the file as an index
record_index = SeqIO.index(os.path.join(root, name), "fasta")
# Loop the dict by gene
for gene_ID, transcript_IDs in id_dict.items():
# Assign the IDs as a string
transcript_IDs_str = ', '.join(transcript_IDs)
# Create a string to store the ortholog
gene_ortholog = ''
# Loop the transcripts
for transcript_ID in transcript_IDs:
# Add the sequence to the database
addSequence(cursor, 'Protein', transcript_ID, record_index[transcript_ID].format("fasta"))
# Check if the current ID is within the genes to ortholog dict
if transcript_ID in transcript_to_ortholog:
# Assign the ortholog
gene_ortholog = transcript_to_ortholog[transcript_ID]
# Check if an ortholog was found
if gene_ortholog:
# Add the gene, with an ortholog
addGeneOrtho(cursor, gene_ID, transcript_IDs_str, gene_ortholog)
else:
# Add the gene, without an ortholog
addGene(cursor, gene_ID, transcript_IDs_str)
# Commit any changes
sqlite_connection.commit()
# Close the connection
cursor.close()