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Added an option do enable/disable N-filtering. #8

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Added an option do enable/disable N-filtering. #8

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6 changes: 3 additions & 3 deletions pyvapor/vaporfunc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@ def parse_and_prefilter(fqs, dbkmers, threshold, k):
f.close()
return reads, nraw

def parse_fasta_uniq(fasta, filter_Ns=True):
def parse_fasta_uniq(fasta, filter_N):
""" Gets unique sequences from a fasta, with filtering of Ns"""
tmph = ""
tmps = ""
Expand All @@ -84,7 +84,7 @@ def parse_fasta_uniq(fasta, filter_Ns=True):
continue
elif l[0] == ">":
if tmps not in sseen and li > 0:
if ((filter_Ns == True) and "N" not in tmps) or filter_Ns == False:
if ((filter_N == True) and "N" not in tmps) or filter_N == False:
hs.append(tmph)
ss.append(tmps)
sseen.add(tmps)
Expand All @@ -94,7 +94,7 @@ def parse_fasta_uniq(fasta, filter_Ns=True):
tmps += l
hs.append(tmph)
ss.append(tmps)
return hs, ss
return hs, ss

def subsample(reads, n):
""" Takes a sample of n from reads """
Expand Down
8 changes: 6 additions & 2 deletions vapor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,9 +49,11 @@

"""

from ctypes.wintypes import BOOLEAN
import sys
import argparse
import os
from xmlrpc.client import boolean
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Those two imports are not needed, isn't it?

import pyvapor as vp

def blockErr():
Expand All @@ -67,8 +69,10 @@ def main(args):
sys.stderr.write("WARNING: kmer sizes of less than 21 can result in contaminating sequence carryover, which may affect results. Only do this if you know your sample is pure, or have increased the filtering threshold -t sufficiently. Refer to the docs for details. \n")

sys.stderr.write("Loading database sequences\n")
seqsh, seqs = vp.parse_fasta_uniq(args.fa)
seqsh, seqs = vp.parse_fasta_uniq(args.fa, args.filter_N)
sys.stderr.write("Got %d unique sequences\n" % len(seqs))
if args.filter_N == False:
sys.stderr.write("WARNING: I WONT TELL YOU WHAT IS AMISS\n")

# Get database kmers for filtering
sys.stderr.write("Getting database kmers\n")
Expand Down Expand Up @@ -149,7 +153,6 @@ def main(args):
group = parser.add_mutually_exclusive_group()
group.add_argument("--return_seqs", action="store_true")
group.add_argument("-o", "--output_prefix", type=str, help="Prefix to write full output to, stout by default", nargs='?', default=None)

parser.add_argument("-q", "--quiet", action="store_true", default=False)
parser.add_argument("--return_best_n", type=int, default=1)
parser.add_argument("-m", "--min_kmer_prop", type=float, help="Minimum proportion of matched kmers allowed for queries [default=0.1]", nargs='?', default=0.1)
Expand All @@ -164,6 +167,7 @@ def main(args):
parser.add_argument("--nocache", action="store_true", default=False)
parser.add_argument("-v", "--version", action="store_true", default=False)
parser.add_argument("--low_mem", action="store_true", default=False)
parser.add_argument("--filter_N", "-n", action="store_true")

if len(sys.argv)==1:
parser.print_help(sys.stderr)
Expand Down