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silva-sampler.py
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silva-sampler.py
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#!/usr/bin/env python3
# !/bin/sh
# Author: Arkadiy Garber
from collections import defaultdict
import re, os
import argparse
import textwrap
import sys
parser = argparse.ArgumentParser(
prog="silva-sampler.py",
formatter_class=argparse.RawDescriptionHelpFormatter,
description=textwrap.dedent('''
Program for sampling sequences from the SILVA database, based on taxanomical resolution;
Developed by Arkadiy Garber; University of Delaware, Geological Sciences
Please send comments and inquiries to arkg@udel.edu
'''))
parser.add_argument('-silva_db', help='location of SILVA database file (in fasta format).')
parser.add_argument('-level', help="Options: phylum (default), class, family, order, genus",
default="phylum")
parser.add_argument('-output', help="Name of output file (i.e. the file containing sampled sequences from SILVA db",
default="silva_sample.fa")
parser.add_argument('-RNA_to_DNA', help="convert uracil nucleotides to thymine? (y/n). Default = n",
default="n")
if len(sys.argv) == 1:
parser.print_help(sys.stderr)
sys.exit(0)
args = parser.parse_known_args()[0]
def main1():
def fastaPhylum(fasta_file):
seq = ''
header = ''
Dict = defaultdict(lambda: defaultdict(lambda: 'EMPTY'))
for i in fasta_file:
i = i.rstrip()
if re.match(r'^>', i):
if len(seq) > 0:
Dict[head]["seq"] = seq
Dict[head]["header"] = header
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
head = headerList[1]
seq = ''
else:
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
head = headerList[1]
seq = ''
else:
seq += i
Dict[head]["seq"] = seq
Dict[head]["header"] = header
outfile = open(args.output, "w")
for j in Dict.keys():
outfile.write(">" + Dict[j]["header"] + "\n")
outfile.write(Dict[j]["seq"] + "\n")
def fastaClass(fasta_file):
seq = ''
header = ''
Dict = defaultdict(lambda: defaultdict(lambda: 'EMPTY'))
for i in fasta_file:
i = i.rstrip()
if re.match(r'^>', i):
if len(seq) > 0:
Dict[head]["seq"] = seq
Dict[head]["header"] = header
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
head = headerList[2]
seq = ''
else:
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
head = headerList[2]
seq = ''
else:
seq += i
Dict[head]["seq"] = seq
Dict[head]["header"] = header
outfile = open(args.output, "w")
for j in Dict.keys():
outfile.write(">" + Dict[j]["header"] + "\n")
outfile.write(Dict[j]["seq"] + "\n")
def fastaOrder(fasta_file):
seq = ''
header = ''
Dict = defaultdict(lambda: defaultdict(lambda: 'EMPTY'))
for i in fasta_file:
i = i.rstrip()
if re.match(r'^>', i):
if len(seq) > 0:
Dict[head]["seq"] = seq
Dict[head]["header"] = header
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
head = headerList[3]
seq = ''
else:
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
head = headerList[3]
seq = ''
else:
seq += i
Dict[head]["seq"] = seq
Dict[head]["header"] = header
outfile = open(args.output, "w")
for j in Dict.keys():
outfile.write(">" + Dict[j]["header"] + "\n")
outfile.write(Dict[j]["seq"] + "\n")
def fastaFamily(fasta_file):
seq = ''
header = ''
Dict = defaultdict(lambda: defaultdict(lambda: 'EMPTY'))
for i in fasta_file:
i = i.rstrip()
if re.match(r'^>', i):
if len(seq) > 0:
Dict[head]["seq"] = seq
Dict[head]["header"] = header
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
head = headerList[4]
seq = ''
else:
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
head = headerList[4]
seq = ''
else:
seq += i
Dict[head]["seq"] = seq
Dict[head]["header"] = header
outfile = open(args.output, "w")
for j in Dict.keys():
outfile.write(">" + Dict[j]["header"] + "\n")
outfile.write(Dict[j]["seq"] + "\n")
def fastaGenus(fasta_file):
seq = ''
header = ''
Dict = defaultdict(lambda: defaultdict(lambda: 'EMPTY'))
for i in fasta_file:
i = i.rstrip()
if re.match(r'^>', i):
if len(seq) > 0:
Dict[head]["seq"] = seq
Dict[head]["header"] = header
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
head = headerList[5]
seq = ''
else:
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
head = headerList[5]
seq = ''
else:
seq += i
Dict[head]["seq"] = seq
Dict[head]["header"] = header
outfile = open(args.output, "w")
for j in Dict.keys():
outfile.write(">" + Dict[j]["header"] + "\n")
outfile.write(Dict[j]["seq"] + "\n")
silva = open(args.silva_db, "r")
if args.level == "phylum":
fastaPhylum(silva)
if args.level == "class":
fastaClass(silva)
if args.level == "order":
fastaOrder(silva)
if args.level == "family":
fastaFamily(silva)
if args.level == "genus":
fastaGenus(silva)
print("Finished sampling from SILVA database.")
print("Thanks for using the silva-sampler program!")
# *************************************************************************************************
# *************************************************************************************************
# *************************************************************************************************
# *************************************************************************************************
# *************************************************************************************************
def main2():
def replace(stringOrlist, list, item):
emptyList = []
for i in stringOrlist:
if i not in list:
emptyList.append(i)
else:
emptyList.append(item)
outString = "".join(emptyList)
return outString
def fastaPhylum(fasta_file):
seq = ''
header = ''
Dict = defaultdict(lambda: defaultdict(lambda: 'EMPTY'))
for i in fasta_file:
i = i.rstrip()
if re.match(r'^>', i):
if len(seq) > 0:
Dict[head]["seq"] = replace(seq, ["U"], "T")
Dict[head]["header"] = header
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
head = headerList[1]
seq = ''
else:
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
head = headerList[1]
seq = ''
else:
seq += i
Dict[head]["seq"] = seq
Dict[head]["header"] = header
outfile = open(args.output, "w")
for j in Dict.keys():
outfile.write(">" + Dict[j]["header"] + "\n")
outfile.write(Dict[j]["seq"] + "\n")
def fastaClass(fasta_file):
seq = ''
header = ''
Dict = defaultdict(lambda: defaultdict(lambda: 'EMPTY'))
for i in fasta_file:
i = i.rstrip()
if re.match(r'^>', i):
if len(seq) > 0:
Dict[head]["seq"] = replace(seq, ["U"], "T")
Dict[head]["header"] = header
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
try:
head = headerList[2]
except IndexError:
pass
seq = ''
else:
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
try:
head = headerList[2]
except IndexError:
pass
seq = ''
else:
seq += i
Dict[head]["seq"] = seq
Dict[head]["header"] = header
outfile = open(args.output, "w")
for j in Dict.keys():
outfile.write(">" + Dict[j]["header"] + "\n")
outfile.write(Dict[j]["seq"] + "\n")
def fastaOrder(fasta_file):
seq = ''
header = ''
Dict = defaultdict(lambda: defaultdict(lambda: 'EMPTY'))
for i in fasta_file:
i = i.rstrip()
if re.match(r'^>', i):
if len(seq) > 0:
Dict[head]["seq"] = replace(seq, ["U"], "T")
Dict[head]["header"] = header
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
try:
head = headerList[3]
except IndexError:
try:
head = headerList[2]
except IndexError:
try:
head = headerList[1]
except IndexError:
pass
seq = ''
else:
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
try:
head = headerList[3]
except IndexError:
try:
head = headerList[2]
except IndexError:
try:
head = headerList[1]
except IndexError:
pass
seq = ''
else:
seq += i
Dict[head]["seq"] = seq
Dict[head]["header"] = header
outfile = open(args.output, "w")
for j in Dict.keys():
outfile.write(">" + Dict[j]["header"] + "\n")
outfile.write(Dict[j]["seq"] + "\n")
def fastaFamily(fasta_file):
seq = ''
header = ''
Dict = defaultdict(lambda: defaultdict(lambda: 'EMPTY'))
for i in fasta_file:
i = i.rstrip()
if re.match(r'^>', i):
if len(seq) > 0:
Dict[head]["seq"] = replace(seq, ["U"], "T")
Dict[head]["header"] = header
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
try:
head = headerList[4]
except IndexError:
try:
head = headerList[3]
except IndexError:
try:
head = headerList[2]
except IndexError:
try:
head = headerList[1]
except IndexError:
pass
seq = ''
else:
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
try:
head = headerList[4]
except IndexError:
try:
head = headerList[3]
except IndexError:
try:
head = headerList[2]
except IndexError:
try:
head = headerList[1]
except IndexError:
pass
seq = ''
else:
seq += i
Dict[head]["seq"] = seq
Dict[head]["header"] = header
outfile = open(args.output, "w")
for j in Dict.keys():
outfile.write(">" + Dict[j]["header"] + "\n")
outfile.write(Dict[j]["seq"] + "\n")
def fastaGenus(fasta_file):
seq = ''
header = ''
Dict = defaultdict(lambda: defaultdict(lambda: 'EMPTY'))
for i in fasta_file:
i = i.rstrip()
if re.match(r'^>', i):
if len(seq) > 0:
Dict[head]["seq"] = replace(seq, ["U"], "T")
Dict[head]["header"] = header
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
try:
head = headerList[5]
except IndexError:
try:
head = headerList[4]
except IndexError:
try:
head = headerList[3]
except IndexError:
try:
head = headerList[2]
except IndexError:
try:
head = headerList[1]
except IndexError:
pass
seq = ''
else:
header = i[1:]
headerLS = header.split(" ")
headerList = headerLS[1].split(";")
try:
head = headerList[5]
except IndexError:
try:
head = headerList[4]
except IndexError:
try:
head = headerList[3]
except IndexError:
try:
head = headerList[2]
except IndexError:
try:
head = headerList[1]
except IndexError:
pass
seq = ''
else:
seq += i
Dict[head]["seq"] = seq
Dict[head]["header"] = header
outfile = open(args.output, "w")
for j in Dict.keys():
outfile.write(">" + Dict[j]["header"] + "\n")
outfile.write(Dict[j]["seq"] + "\n")
silva = open(args.silva_db, "r")
if args.level == "phylum":
fastaPhylum(silva)
if args.level == "class":
fastaClass(silva)
if args.level == "order":
fastaOrder(silva)
if args.level == "family":
fastaFamily(silva)
if args.level == "genus":
fastaGenus(silva)
print("Finished sampling from SILVA database.")
print("Thanks for using the silva-sampler program!")
if args.RNA_to_DNA == "n":
main1()
if args.RNA_to_DNA == "y":
main2()