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test_demultiplex.py
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test_demultiplex.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Aim: test demultiplex.py
# Copyright (C) 2014-2017 Institut National de la Recherche Agronomique
# License: GPL-3+
# Persons: Timothée Flutre [cre,aut], Laurène Gay [ctb], Nicolas Rode [ctb]
# Versioning: https://github.com/timflutre/quantgen
# to allow code to work with Python 2 and 3
from __future__ import print_function # print is a function in python3
from __future__ import unicode_literals # avoid adding "u" to each string
from __future__ import division # avoid writing float(x) when dividing by x
import sys
import os
import getopt
import time
import datetime
from subprocess import Popen, PIPE, check_output
import math
import gzip
import tempfile
import shutil
import itertools
if sys.version_info[0] == 2:
if sys.version_info[1] < 7:
msg = "ERROR: Python should be in version 2.7 or higher"
sys.stderr.write("%s\n\n" % msg)
sys.exit(1)
from Bio import SeqIO
from Bio.Alphabet import IUPAC
from Bio.Data.IUPACData import ambiguous_dna_values
progVersion = "1.11.0" # http://semver.org/
class TestDemultiplex(object):
def __init__(self):
self.verbose = 0
self.pathToProg = ""
self.testsToRun = ["1", "2", "4a", "4b", "4c", "4d", "chim", "subst",
"4a_s", "mult"]
self.clean = True
def help(self):
"""
Display the help on stdout.
The format complies with help2man (http://www.gnu.org/s/help2man)
"""
msg = "`%s' tests demultiplex.py.\n" % os.path.basename(sys.argv[0])
msg += "\n"
msg += "Usage: %s [OPTIONS] ...\n" % os.path.basename(sys.argv[0])
msg += "\n"
msg += "Options:\n"
msg += " -h, --help\tdisplay the help and exit\n"
msg += " -V, --version\toutput version information and exit\n"
msg += " -v, --verbose\tverbosity level (default=0/1/2/3)\n"
msg += " -p, --p2p\tfull path to the program to be tested\n"
msg += " -t, --test\tidentifiers of test(s) to run (default=1-2-4a-4b-4c-4d-chim-subst-4a_s-mult)\n"
msg += " -n, --noclean\tkeep temporary directory with all files\n"
msg += "\n"
msg += "Examples:\n"
msg += " %s -p ~/src/demultiplex.py -n\n" % os.path.basename(sys.argv[0])
msg += "\n"
msg += "Report bugs to <[email protected]>."
print(msg); sys.stdout.flush()
def version(self):
"""
Display version and license information on stdout.
The person roles complies with R's guidelines (The R Journal Vol. 4/1, June 2012).
"""
msg = "%s %s\n" % (os.path.basename(sys.argv[0]), progVersion)
msg += "\n"
msg += "Copyright (C) 2014-2017 Institut National de la Recherche Agronomique (INRA).\n"
msg += "License GPL-3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>\n"
msg += "\n"
msg += "Written by Timothée Flutre [cre,aut], Laurène Gay [ctb], Nicolas Rode [ctb]."
print(msg.encode("utf8")); sys.stdout.flush()
def setAttributesFromCmdLine(self):
"""
Parse the command-line arguments.
"""
try:
opts, args = getopt.getopt( sys.argv[1:], "hVv:p:t:n",
["help", "version", "verbose=",
"p2p=", "test=", "noclean"])
except getopt.GetoptError as err:
sys.stderr.write("%s\n\n" % str(err))
self.help()
sys.exit(2)
for o, a in opts:
if o == "-h" or o == "--help":
self.help()
sys.exit(0)
elif o == "-V" or o == "--version":
self.version()
sys.exit(0)
elif o == "-v" or o == "--verbose":
self.verbose = int(a)
elif o == "-p" or o == "--p2p":
self.pathToProg = a
elif o == "-t" or o == "--test":
self.testsToRun = a.split("-")
elif o == "-n" or o == "--noclean":
self.clean = False
else:
assert False, "invalid option"
def checkAttributes(self):
"""
Check the values of the command-line parameters.
"""
if self.pathToProg == "":
msg = "ERROR: missing compulsory option --p2p"
sys.stderr.write("%s\n\n" % msg)
self.help()
sys.exit(1)
if not os.path.exists(self.pathToProg):
msg = "ERROR: can't find file %s" % self.pathToProg
sys.stderr.write("%s\n\n" % msg)
self.help()
sys.exit(1)
for t in self.testsToRun:
if t not in ["1", "2", "4a", "4b", "4c", "4d", "chim", "subst",
"4a_s", "mult"]:
msg = "ERROR: unknown --test %s" % t
sys.stderr.write("%s\n\n" % msg)
self.help()
sys.exit(1)
#==========================================================================
def beforeTest(self):
"""
Create a temporary folder with a unique ID
"""
cwd = os.getcwd()
testDir = tempfile.mkdtemp(dir=cwd, prefix="tmp_test_")
os.chdir(testDir)
if self.verbose > 0:
print("temp dir: %s" % os.getcwd()); sys.stdout.flush()
return cwd, testDir
def writeTagFile(self, it, fmt="fasta", multInd4=False):
with open(it, "w") as itHandle:
if fmt == "fasta":
txt = ">ind1\nAAA\n"
txt += ">ind2\nTTT\n"
txt += ">ind3\nGGG\n"
txt += ">ind4\nCCC\n"
if multInd4:
txt += ">ind4\nAATTGGC\n"
elif fmt == "table":
txt = "id\ttag\n"
txt += "ind1\tAAA\n"
txt += "ind2\tTTT\n"
txt += "ind3\tGGG\n"
txt += "ind4\tCCC\n"
if multInd4:
txt += "ind4\tAATTGGC\n"
itHandle.write(txt)
def launchProg(self, ifq1, ifq2, it, met, dist, re, chim, nci, subst):
"""
Launch demultiplex.py with the 'args' arguments
"""
args = [self.pathToProg,
"--idir", "./",
"--ifq1", ifq1]
if ifq2 != None:
args += ["--ifq2", ifq2]
args += ["--it", it,
"--ofqp", "test",
"--met", met,
"--dist", str(dist),
"--chim", str(chim),
"-v", str(self.verbose - 1)]
if re != "":
args += ["--re", re]
if nci:
args += ["--nci"]
if subst > 0:
args += ["--subst", str(subst)]
if self.verbose > 0:
print(" ".join(args))
# msgs = check_output(args)
msgs = Popen(args, stdout=PIPE, stderr=PIPE).communicate()
if self.verbose > 1:
if msgs[0] != "":
print("stdout:")
print(msgs[0][:-1])
if msgs[1] != "":
print("sterr:")
print(msgs[1][:-1])
return msgs
def afterTest(self, cwd, testDir):
os.chdir(cwd)
if self.clean:
shutil.rmtree(testDir)
#==========================================================================
def test_met1_prepare(self):
ifq1 = "reads_R1.fastq.gz"
ifq2 = "reads_R2.fastq.gz"
ifq1Handle = gzip.open(ifq1, "w")
ifq2Handle = gzip.open(ifq2, "w")
# pair 1: both reads have perfect tag of ind 2 at bp 1
txt = "@INST1:1:FLOW1:2:2104:15343:197391 1:N:0\n"
txt += "TTT" # tag
txt += "TCAACCTGGAGTTCCAC\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~\n"
ifq1Handle.write(txt)
txt = "@INST1:1:FLOW1:2:2104:15343:197391 2:N:0\n"
txt += "TTT" # tag
txt += "GTAGCTGAGATCGGAAG\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~\n"
ifq2Handle.write(txt)
# pair 2: only read 1 has perfect tag of ind 1 at bp 1
txt = "@INST1:1:FLOW1:2:2104:15343:197392 1:N:0\n"
txt += "AAA" # tag
txt += "TCAACCTGGAGTTCCAC\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~\n"
ifq1Handle.write(txt)
txt = "@INST1:1:FLOW1:2:2104:15343:197392 2:N:0\n"
txt += "ATA" # tag
txt += "GTAGCTGAGATCGGAAG\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~\n"
ifq2Handle.write(txt)
ifq1Handle.close()
ifq2Handle.close()
for f in ["test_ind2_R1.fastq.gz", "test_ind2_R2.fastq.gz",
"test_unassigned_R1.fastq.gz", "test_unassigned_R2.fastq.gz"]:
if os.path.isfile(f):
os.remove(f)
it = "tags.fa"
self.writeTagFile(it)
return ifq1, ifq2, it
def test_met1_comp(self, msgs):
if not os.path.exists("test_ind2_R1.fastq.gz") \
or not os.path.exists("test_ind2_R2.fastq.gz"):
print("test_met1: fail (1)")
return
else:
with gzip.open("test_ind2_R1.fastq.gz") as inFqHandle1, \
gzip.open("test_ind2_R2.fastq.gz") as inFqHandle2:
reads1 = SeqIO.parse(inFqHandle1, "fastq",
alphabet=IUPAC.ambiguous_dna)
reads2 = SeqIO.parse(inFqHandle2, "fastq",
alphabet=IUPAC.ambiguous_dna)
for (read1, read2) in itertools.izip(reads1, reads2):
if read1.id != "INST1:1:FLOW1:2:2104:15343:197391" and \
read2.id != "INST1:1:FLOW1:2:2104:15343:197391":
print("test_met1: fail (2)")
return
if str(read1.seq) != "TCAACCTGGAGTTCCAC" or \
str(read2.seq) != "GTAGCTGAGATCGGAAG":
print("test_met1: fail (3)")
return
if os.path.exists("test_ind1_R1.fastq.gz") or \
os.path.exists("test_ind1_R2.fastq.gz"):
print("test_met1: fail (3)")
return
print("test_met1: pass")
def test_met1(self):
if self.verbose > 0:
print("launch test met1 ...")
sys.stdout.flush()
cwd, testDir = self.beforeTest()
ifq1, ifq2, it = self.test_met1_prepare()
msgs = self.launchProg(ifq1, ifq2, it, met="1", dist=0, re="",
chim="0", nci=False, subst=0)
self.test_met1_comp(msgs)
self.afterTest(cwd, testDir)
#==========================================================================
def test_met2_comp(self, msgs):
if not os.path.exists("test_ind2_R1.fastq.gz") or \
not os.path.exists("test_ind2_R2.fastq.gz") or \
not os.path.exists("test_ind1_R1.fastq.gz") or \
not os.path.exists("test_ind1_R2.fastq.gz"):
print("test_met2: fail (1)")
return
else:
with gzip.open("test_ind2_R1.fastq.gz") as inFqHandle1, \
gzip.open("test_ind2_R2.fastq.gz") as inFqHandle2:
l1 = list(SeqIO.parse(inFqHandle1, "fastq",
alphabet=IUPAC.ambiguous_dna))
l2 = list(SeqIO.parse(inFqHandle2, "fastq",
alphabet=IUPAC.ambiguous_dna))
if len(l1) != 1 or len(l2) != 1:
print("test_met2: fail (2)")
return
if l1[0].id != "INST1:1:FLOW1:2:2104:15343:197391" or \
l2[0].id != "INST1:1:FLOW1:2:2104:15343:197391":
print("test_met2: fail (3)")
return
if str(l1[0].seq) != "TCAACCTGGAGTTCCAC" or \
str(l2[0].seq) != "GTAGCTGAGATCGGAAG":
print("test_met1: fail (4)")
return
with gzip.open("test_ind1_R1.fastq.gz") as inFqHandle1, \
gzip.open("test_ind1_R2.fastq.gz") as inFqHandle2:
l1 = list(SeqIO.parse(inFqHandle1, "fastq",
alphabet=IUPAC.ambiguous_dna))
l2 = list(SeqIO.parse(inFqHandle2, "fastq",
alphabet=IUPAC.ambiguous_dna))
if len(l1) != 1 or len(l2) != 1:
print("test_met2: fail (5)")
return
if l1[0].id != "INST1:1:FLOW1:2:2104:15343:197392" or \
l2[0].id != "INST1:1:FLOW1:2:2104:15343:197392":
print("test_met2: fail (6)")
return
if str(l1[0].seq) != "TCAACCTGGAGTTCCAC" or \
str(l2[0].seq) != "ATAGTAGCTGAGATCGGAAG":
print("test_met1: fail (7)")
return
print("test_met2: pass")
def test_met2(self):
if self.verbose > 0:
print("launch test met2 ...")
sys.stdout.flush()
cwd, testDir = self.beforeTest()
ifq1, ifq2, it = self.test_met1_prepare()
msgs = self.launchProg(ifq1, ifq2, it, met="2", dist=0, re="",
chim="0", nci=False, subst=0)
self.test_met2_comp(msgs)
self.afterTest(cwd, testDir)
#==========================================================================
def test_met4_prepare(self):
ifq1 = "reads_R1.fastq.gz"
ifq2 = "reads_R2.fastq.gz"
ifq1Handle = gzip.open(ifq1, "w")
ifq2Handle = gzip.open(ifq2, "w")
# pair 1: read 1 has perfect tag of ind 2 at bp 1; read 2 has no tag
txt = "@INST1:1:FLOW1:2:2104:15343:197391 1:N:0\n"
txt += "TTT" # tag
txt += "TCAACCTGGAGTTCCAC\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~\n"
ifq1Handle.write(txt)
txt = "@INST1:1:FLOW1:2:2104:15343:197391 2:N:0\n"
txt += ""
txt += "GTAGCTGAGATCGGAAG\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~\n"
ifq2Handle.write(txt)
# pair 2: read 1 has perfect tag of ind 1 but at bp 2; read 2 has no tag
txt = "@INST1:1:FLOW1:2:2104:15343:197392 1:N:0\n"
txt += "TAAA" # tag with a 1-bp shift
txt += "TAGCTACATHACTACAT\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~~\n"
ifq1Handle.write(txt)
txt = "@INST1:1:FLOW1:2:2104:15343:197392 2:N:0\n"
txt += ""
txt += "CTCAGCTGGACTCGACT\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~\n"
ifq2Handle.write(txt)
ifq1Handle.close()
ifq2Handle.close()
for f in ["test_ind2_R1.fastq.gz", "test_ind2_R2.fastq.gz",
"test_unassigned_R1.fastq.gz", "test_unassigned_R2.fastq.gz"]:
if os.path.isfile(f):
os.remove(f)
it = "tags.fa"
self.writeTagFile(it)
return ifq1, ifq2, it
def test_met4a_comp(self, msgs):
if not os.path.exists("test_ind2_R1.fastq.gz") or \
not os.path.exists("test_ind2_R2.fastq.gz"):
print("test_met4a: fail (1)")
return
else:
with gzip.open("test_ind2_R1.fastq.gz") as inFqHandle1, \
gzip.open("test_ind2_R2.fastq.gz") as inFqHandle2:
l1 = list(SeqIO.parse(inFqHandle1, "fastq",
alphabet=IUPAC.ambiguous_dna))
l2 = list(SeqIO.parse(inFqHandle2, "fastq",
alphabet=IUPAC.ambiguous_dna))
if len(l1) != 1 or len(l2) != 1:
print("test_met4a: fail (2)")
return
if l1[0].id != "INST1:1:FLOW1:2:2104:15343:197391" or \
l2[0].id != "INST1:1:FLOW1:2:2104:15343:197391":
print("test_met4a: fail (3)")
return
if str(l1[0].seq) != "TCAACCTGGAGTTCCAC" or \
str(l2[0].seq) != "GTAGCTGAGATCGGAAG":
print("test_met4a: fail (4)")
return
if os.path.exists("test_ind1_R1.fastq.gz") or \
os.path.exists("test_ind1_R2.fastq.gz"):
print("test_met4a: fail (5)")
return
print("test_met4a: pass")
def test_met4a(self):
if self.verbose > 0:
print("launch test met4a ...")
sys.stdout.flush()
cwd, testDir = self.beforeTest()
ifq1, ifq2, it = self.test_met4_prepare()
msgs = self.launchProg(ifq1, ifq2, it, met="4a", dist=0, re="",
chim="0", nci=False, subst=0)
self.test_met4a_comp(msgs)
self.afterTest(cwd, testDir)
#==========================================================================
def test_met4b_comp(self, msgs):
if not os.path.exists("test_ind2_R1.fastq.gz") or \
not os.path.exists("test_ind2_R2.fastq.gz"):
print("test_met4b: fail (1)")
return
else:
with gzip.open("test_ind2_R1.fastq.gz") as inFqHandle1, \
gzip.open("test_ind2_R2.fastq.gz") as inFqHandle2:
l1 = list(SeqIO.parse(inFqHandle1, "fastq",
alphabet=IUPAC.ambiguous_dna))
l2 = list(SeqIO.parse(inFqHandle2, "fastq",
alphabet=IUPAC.ambiguous_dna))
if len(l1) != 1 or len(l2) != 1:
print("test_met4b: fail (2)")
return
if l1[0].id != "INST1:1:FLOW1:2:2104:15343:197391" or \
l2[0].id != "INST1:1:FLOW1:2:2104:15343:197391":
print("test_met4b: fail (3)")
return
if str(l1[0].seq) != "TCAACCTGGAGTTCCAC" or \
str(l2[0].seq) != "GTAGCTGAGATCGGAAG":
print("test_met4b: fail (4)")
return
if not os.path.exists("test_ind1_R1.fastq.gz") or \
not os.path.exists("test_ind1_R2.fastq.gz"):
print("test_met4b: fail (5)")
return
else:
with gzip.open("test_ind1_R1.fastq.gz") as inFqHandle1, \
gzip.open("test_ind1_R2.fastq.gz") as inFqHandle2:
l1 = list(SeqIO.parse(inFqHandle1, "fastq",
alphabet=IUPAC.ambiguous_dna))
l2 = list(SeqIO.parse(inFqHandle2, "fastq",
alphabet=IUPAC.ambiguous_dna))
if len(l1) != 1 or len(l2) != 1:
print("test_met4b: fail (6)")
return
if l1[0].id != "INST1:1:FLOW1:2:2104:15343:197392" or \
l2[0].id != "INST1:1:FLOW1:2:2104:15343:197392":
print("test_met4b: fail (7)")
return
if str(l1[0].seq) != "TAGCTACATHACTACAT" or \
str(l2[0].seq) != "CTCAGCTGGACTCGACT":
print("test_met4b: fail (8)")
return
print("test_met4b: pass")
def test_met4b(self):
if self.verbose > 0:
print("launch test met4b ...")
sys.stdout.flush()
cwd, testDir = self.beforeTest()
ifq1, ifq2, it = self.test_met4_prepare()
msgs = self.launchProg(ifq1, ifq2, it, met="4b", dist=10, re="",
chim="0", nci=False, subst=0)
self.test_met4b_comp(msgs)
self.afterTest(cwd, testDir)
#==========================================================================
def test_met4c_prepare(self):
ifq1 = "reads_R1.fastq.gz"
ifq2 = "reads_R2.fastq.gz"
ifq1Handle = gzip.open(ifq1, "w")
ifq2Handle = gzip.open(ifq2, "w")
# pair 1: read 1 has perfect tag and cut site of ind 2 at bp 2; read 2 has no tag
txt = "@INST1:1:FLOW1:2:2104:15343:197391 1:N:0\n"
txt += "ATTT" # tag with a 1-bp shift
txt += "CAGCCCTGGAGTTCCAC\n" # insert with ApekI cut site
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~~\n"
ifq1Handle.write(txt)
txt = "@INST1:1:FLOW1:2:2104:15343:197391 2:N:0\n"
txt += ""
txt += "GTAGCTGAGATCGGAAG\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~\n"
ifq2Handle.write(txt)
# pair 2: read 1 has perfect tag of ind 1 at bp 2 but no cut site; read 2 has no tag
txt = "@INST1:1:FLOW1:2:2104:15343:197392 1:N:0\n"
txt += "TAAA" # tag with a 1-bp shift
txt += "TAGCTACATHACTACAT\n" # insert with no ApekI cut site
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~~\n"
ifq1Handle.write(txt)
txt = "@INST1:1:FLOW1:2:2104:15343:197392 2:N:0\n"
txt += ""
txt += "CTCAGCTGGACTCGACT\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~\n"
ifq2Handle.write(txt)
ifq1Handle.close()
ifq2Handle.close()
for f in ["test_ind2_R1.fastq.gz", "test_ind2_R2.fastq.gz",
"test_unassigned_R1.fastq.gz", "test_unassigned_R2.fastq.gz"]:
if os.path.isfile(f):
os.remove(f)
it = "tags.fa"
self.writeTagFile(it)
return ifq1, ifq2, it
def test_met4c_comp(self, msgs):
if not os.path.exists("test_ind2_R1.fastq.gz") or \
not os.path.exists("test_ind2_R2.fastq.gz"):
print("test_met4c: fail (1)")
return
else:
with gzip.open("test_ind2_R1.fastq.gz") as inFqHandle1, \
gzip.open("test_ind2_R2.fastq.gz") as inFqHandle2:
l1 = list(SeqIO.parse(inFqHandle1, "fastq",
alphabet=IUPAC.ambiguous_dna))
l2 = list(SeqIO.parse(inFqHandle2, "fastq",
alphabet=IUPAC.ambiguous_dna))
if len(l1) != 1 or len(l2) != 1:
print("test_met4c: fail (2)")
return
if l1[0].id != "INST1:1:FLOW1:2:2104:15343:197391" or \
l2[0].id != "INST1:1:FLOW1:2:2104:15343:197391":
print("test_met4c: fail (3)")
return
if str(l1[0].seq) != "CAGCCCTGGAGTTCCAC" or \
str(l2[0].seq) != "GTAGCTGAGATCGGAAG":
print("test_met4c: fail (4)")
return
if os.path.exists("test_ind1_R1.fastq.gz") or \
os.path.exists("test_ind1_R2.fastq.gz"):
print("test_met4c: fail (5)")
return
print("test_met4c: pass")
def test_met4c(self):
if self.verbose > 0:
print("launch test met4c ...")
sys.stdout.flush()
cwd, testDir = self.beforeTest()
ifq1, ifq2, it = self.test_met4c_prepare()
msgs = self.launchProg(ifq1, ifq2, it, met="4c", dist=10, re="ApeKI",
chim="0", nci=False, subst=0)
self.test_met4c_comp(msgs)
self.afterTest(cwd, testDir)
#==========================================================================
def test_met4d_prepare(self):
ifq1 = "reads_R1.fastq.gz"
ifq2 = "reads_R2.fastq.gz"
ifq1Handle = gzip.open(ifq1, "w")
ifq2Handle = gzip.open(ifq2, "w")
# pair 1: read 1 has perfect tag and cut site of ind 4 at bp 2; read 2 has the tag but not the cut site
txt = "@INST1:1:FLOW1:2:2104:15343:197391 1:N:0\n"
txt += "ATTT" # tag with a 1-bp shift
txt += "CAGCCCTGGAGTTCCAC\n" # insert with ApekI cut site
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~~\n"
ifq1Handle.write(txt)
txt = "@INST1:1:FLOW1:2:2104:15343:197391 2:N:0\n"
txt += "ATTT" # tag with a 1-bp shift
txt += "GTAGCTGAGATCGGAAG\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~~\n"
ifq2Handle.write(txt)
# pair 2: read 1 has perfect tag of ind 1 at bp 2 but wrong cut site; read 2 has tag of ind 1 and the right cut site
txt = "@INST1:1:FLOW1:2:2104:15343:197392 1:N:0\n"
txt += "TAAA" # tag with a 1-bp shift
txt += "TAGCTACATAACTACAT\n" # insert with no ApekI cut site
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~~\n"
ifq1Handle.write(txt)
txt = "@INST1:1:FLOW1:2:2104:15343:197392 2:N:0\n"
txt += "TAAA" # tag with a 1-bp shift
txt += "CAGCCCTGGAGTTCCAA\n" # insert with ApekI cut site
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~~\n"
ifq2Handle.write(txt)
# pair 3: read 1 has perfect tag of ind 3 at bp 2 but wrong cut site; read 2 has wrong tag but right cut site
txt = "@INST1:1:FLOW1:2:2104:15343:197393 1:N:0\n"
txt += "TGGG" # tag with a 1-bp shift
txt += "TAGCTACATTTACTACT\n" # insert with no ApekI cut site
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~~\n"
ifq1Handle.write(txt)
txt = "@INST1:1:FLOW1:2:2104:15343:197393 2:N:0\n"
txt += "TGTG" # tag with a 1-bp shift
txt += "CAGCCCTGGAGTTCCAG\n" # insert with ApekI cut site
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~~\n"
ifq2Handle.write(txt)
# pair 4: chimera; read 1 has the perfect tag and cut site of ind 3 at bp 2; read 2 has the perfect tag and cut site of ind 1
txt = "@INST1:1:FLOW1:2:2104:15343:197394 1:N:0\n"
txt += "TGGG" # tag without shift
txt += "CAGCCCTGGAGTTCCAG\n" # ApekI cut site
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~~\n"
ifq1Handle.write(txt)
txt = "@INST1:1:FLOW1:2:2104:15343:197394 2:N:0\n"
txt += "TAAA" # tag with a 1-bp shift
txt += "CTGCTACATTTACTACT\n" # insert with ApekI cut site
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~~\n"
ifq2Handle.write(txt)
ifq1Handle.close()
ifq2Handle.close()
for f in ["test_ind1_R1.fastq.gz", "test_ind1_R2.fastq.gz",
"test_ind2_R1.fastq.gz", "test_ind2_R2.fastq.gz",
"test_unassigned_R1.fastq.gz", "test_unassigned_R2.fastq.gz"]:
if os.path.isfile(f):
os.remove(f)
it = "tags.fa"
self.writeTagFile(it)
return ifq1, ifq2, it
def test_met4d_comp(self, msgs):
testId = 1
if not os.path.exists("test_ind1_R1.fastq.gz") or \
not os.path.exists("test_ind1_R2.fastq.gz") or \
not os.path.exists("test_ind2_R1.fastq.gz") or \
not os.path.exists("test_ind2_R2.fastq.gz") or \
os.path.exists("test_ind3_R1.fastq.gz") or \
os.path.exists("test_ind3_R2.fastq.gz") or \
not os.path.exists("test_chimeras_R1.fastq.gz") or \
not os.path.exists("test_chimeras_R2.fastq.gz"):
print("test_met4d: fail (%i)" % testId)
return
testId += 1
with gzip.open("test_ind1_R1.fastq.gz") as inFqHandle1, \
gzip.open("test_ind1_R2.fastq.gz") as inFqHandle2:
l1 = list(SeqIO.parse(inFqHandle1, "fastq",
alphabet=IUPAC.ambiguous_dna))
l2 = list(SeqIO.parse(inFqHandle2, "fastq",
alphabet=IUPAC.ambiguous_dna))
if len(l1) != 1 or len(l2) != 1:
print("test_met4d: fail (%i)" % testId)
return
testId += 1
if l1[0].id != "INST1:1:FLOW1:2:2104:15343:197392" or \
l2[0].id != "INST1:1:FLOW1:2:2104:15343:197392":
print("test_met4d: fail (%i)" % testId)
return
testId += 1
if str(l1[0].seq) != "TAGCTACATAACTACAT" or \
str(l2[0].seq) != "CAGCCCTGGAGTTCCAA":
print("test_met4d: fail (%i)" % testId)
return
testId += 1
with gzip.open("test_ind2_R1.fastq.gz") as inFqHandle1, \
gzip.open("test_ind2_R2.fastq.gz") as inFqHandle2:
l1 = list(SeqIO.parse(inFqHandle1, "fastq",
alphabet=IUPAC.ambiguous_dna))
l2 = list(SeqIO.parse(inFqHandle2, "fastq",
alphabet=IUPAC.ambiguous_dna))
if len(l1) != 1 or len(l2) != 1:
print("test_met4d: fail (%i)" % testId)
return
testId += 1
if l1[0].id != "INST1:1:FLOW1:2:2104:15343:197391" or \
l2[0].id != "INST1:1:FLOW1:2:2104:15343:197391":
print("test_met4d: fail (%i)" % testId)
return
testId += 1
if str(l1[0].seq) != "CAGCCCTGGAGTTCCAC" or \
str(l2[0].seq) != "GTAGCTGAGATCGGAAG":
print("test_met4d: fail (%i)" % testId)
return
testId += 1
with gzip.open("test_chimeras_R1.fastq.gz") as inFqHandle1, \
gzip.open("test_chimeras_R2.fastq.gz") as inFqHandle2:
l1 = list(SeqIO.parse(inFqHandle1, "fastq",
alphabet=IUPAC.ambiguous_dna))
l2 = list(SeqIO.parse(inFqHandle2, "fastq",
alphabet=IUPAC.ambiguous_dna))
if len(l1) != 1 or len(l2) != 1:
print("test_met4d: fail (%i)" % testId)
return
testId += 1
if l1[0].id != "INST1:1:FLOW1:2:2104:15343:197394" or \
l2[0].id != "INST1:1:FLOW1:2:2104:15343:197394":
print("test_met4d: fail (%i)" % testId)
return
testId += 1
print("test_met4d: pass")
def test_met4d(self):
if self.verbose > 0:
print("launch test met4d ...")
sys.stdout.flush()
cwd, testDir = self.beforeTest()
ifq1, ifq2, it = self.test_met4d_prepare()
msgs = self.launchProg(ifq1, ifq2, it, met="4d", dist=10, re="ApeKI",
chim="0", nci=False, subst=0)
self.test_met4d_comp(msgs)
self.afterTest(cwd, testDir)
#==========================================================================
def test_chim_prepare(self):
ifq1 = "reads_R1.fastq.gz"
ifq2 = "reads_R2.fastq.gz"
ifq1Handle = gzip.open(ifq1, "w")
ifq2Handle = gzip.open(ifq2, "w")
# pair 1: both reads have perfect tag of ind 2 at bp 1, and no chimera
txt = "@INST1:1:FLOW1:2:2104:15343:197391 1:N:0\n"
txt += "TTT" # tag
txt += "TCAACCTGGAGTTCCAC\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~\n"
ifq1Handle.write(txt)
txt = "@INST1:1:FLOW1:2:2104:15343:197391 2:N:0\n"
txt += "TTT" # tag
txt += "GTAGCTGAGATCGGAAG\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~\n"
ifq2Handle.write(txt)
# pair 2: read R1 is a chimera (start at the 9-th nucleotide)
txt = "@INST1:1:FLOW1:2:2104:15343:197392 1:N:0\n"
txt += "AAA" # tag
txt += "TCAACGCAGCGTTCCAC\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~\n"
ifq1Handle.write(txt)
txt = "@INST1:1:FLOW1:2:2104:15343:197392 2:N:0\n"
txt += "AAA" # tag
txt += "GTAGCTGAGATCGGAAG\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~\n"
ifq2Handle.write(txt)
ifq1Handle.close()
ifq2Handle.close()
for f in ["test_ind2_R1.fastq.gz", "test_ind2_R2.fastq.gz",
"test_unassigned_R1.fastq.gz", "test_unassigned_R2.fastq.gz",
"test_chimeras_R1.fastq.gz", "test_chimeras_R2.fastq.gz"]:
if os.path.isfile(f):
os.remove(f)
it = "tags.fa"
self.writeTagFile(it)
return ifq1, ifq2, it
def test_chim_comp(self, msgs):
testId = 1
if not os.path.exists("test_ind2_R1.fastq.gz") \
or not os.path.exists("test_ind2_R2.fastq.gz") \
or not os.path.exists("test_chimeras_R1.fastq.gz") \
or not os.path.exists("test_chimeras_R2.fastq.gz"):
print("test_chim: fail (%s)" % testId)
return
testId += 1
with gzip.open("test_ind2_R1.fastq.gz") as inFqHandle1, \
gzip.open("test_ind2_R2.fastq.gz") as inFqHandle2:
reads1 = SeqIO.parse(inFqHandle1, "fastq",
alphabet=IUPAC.ambiguous_dna)
reads2 = SeqIO.parse(inFqHandle2, "fastq",
alphabet=IUPAC.ambiguous_dna)
for (read1, read2) in itertools.izip(reads1, reads2):
if read1.id != "INST1:1:FLOW1:2:2104:15343:197391" and \
read2.id != "INST1:1:FLOW1:2:2104:15343:197391":
print("test_chim: fail (%s)" % testId)
return
testId += 1
if str(read1.seq) != "TCAACCTGGAGTTCCAC" or \
str(read2.seq) != "GTAGCTGAGATCGGAAG":
print("test_chim: fail (%s)" % testId)
return
testId += 1
with gzip.open("test_chimeras_R1.fastq.gz") as inFqHandle1, \
gzip.open("test_chimeras_R2.fastq.gz") as inFqHandle2:
reads1 = SeqIO.parse(inFqHandle1, "fastq",
alphabet=IUPAC.ambiguous_dna)
reads2 = SeqIO.parse(inFqHandle2, "fastq",
alphabet=IUPAC.ambiguous_dna)
for (read1, read2) in itertools.izip(reads1, reads2):
if read1.id != "INST1:1:FLOW1:2:2104:15343:197392" and \
read2.id != "INST1:1:FLOW1:2:2104:15343:197392":
print("test_chim: fail (%s)" % testId)
return
testId += 1
if str(read1.seq) != "AAATCAACGCAGCGTTCCAC" or \
str(read2.seq) != "AAAGTAGCTGAGATCGGAAG":
print("test_chim: fail (%s)" % testId)
return
testId += 1
print("test_chim: pass")
def test_chim(self):
if self.verbose > 0:
print("launch test chim ...")
sys.stdout.flush()
cwd, testDir = self.beforeTest()
ifq1, ifq2, it = self.test_chim_prepare()
msgs = self.launchProg(ifq1, ifq2, it, met="1", dist=0, re="ApeKI",
chim="2", nci=False, subst=0)
self.test_chim_comp(msgs)
self.afterTest(cwd, testDir)
#==========================================================================
def test_subst_prepare(self):
ifq1 = "reads_R1.fastq.gz"
ifq2 = "reads_R2.fastq.gz"
ifq1Handle = gzip.open(ifq1, "w")
ifq2Handle = gzip.open(ifq2, "w")
# pair 1: read 1 has perfect tag and cut site of ind 2 at bp 2; read 2 has no tag
txt = "@INST1:1:FLOW1:2:2104:15343:197391 1:N:0\n"
txt += "ATTT" # tag with a 1-bp shift
txt += "CAGCCCTGGAGTTCCAC\n" # insert with ApekI cut site
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~~\n"
ifq1Handle.write(txt)
txt = "@INST1:1:FLOW1:2:2104:15343:197391 2:N:0\n"
txt += ""
txt += "GTAGCTGAGATCGGAAG\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~\n"
ifq2Handle.write(txt)
# pair 2: read 1 has perfect tag of ind 1 at bp 2 but no cut site; read 2 has no tag
txt = "@INST1:1:FLOW1:2:2104:15343:197392 1:N:0\n"
txt += "TAAA" # tag with a 1-bp shift
txt += "TTTCTACATHACTACAT\n" # insert with no ApekI cut site
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~~\n"
ifq1Handle.write(txt)
txt = "@INST1:1:FLOW1:2:2104:15343:197392 2:N:0\n"
txt += ""
txt += "CTCAGCTGGACTCGACT\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~\n"
ifq2Handle.write(txt)
# pair 3: read 1 has perfect tag and cut site (with an N) of ind 2 at bp 2; read 2 has no tag
txt = "@INST1:1:FLOW1:2:2104:15343:197393 1:N:0\n"
txt += "ATTT" # tag with a 1-bp shift
txt += "CANCCCTGGAGTTCCAC\n" # insert with ApekI cut site with an N
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~~~~~\n"
ifq1Handle.write(txt)
txt = "@INST1:1:FLOW1:2:2104:15343:197393 2:N:0\n"
txt += ""
txt += "GTAGCTGAGATCGGAAG\n" # insert
txt += "+\n"
txt += "~~~~~~~~~~~~~~~~~\n"
ifq2Handle.write(txt)
ifq1Handle.close()
ifq2Handle.close()
for f in ["test_ind2_R1.fastq.gz", "test_ind2_R2.fastq.gz",
"test_unassigned_R1.fastq.gz", "test_unassigned_R2.fastq.gz"]:
if os.path.isfile(f):
os.remove(f)
it = "tags.fa"
self.writeTagFile(it)
return ifq1, ifq2, it
def test_subst_comp(self, msgs):
if not os.path.exists("test_ind2_R1.fastq.gz") or \
not os.path.exists("test_ind2_R2.fastq.gz"):
print("test_subst: fail (1)")
return
else:
with gzip.open("test_ind2_R1.fastq.gz") as inFqHandle1, \
gzip.open("test_ind2_R2.fastq.gz") as inFqHandle2:
l1 = list(SeqIO.parse(inFqHandle1, "fastq",
alphabet=IUPAC.ambiguous_dna))
l2 = list(SeqIO.parse(inFqHandle2, "fastq",
alphabet=IUPAC.ambiguous_dna))
if len(l1) != 2 or len(l2) != 2:
print("test_subst: fail (2)")
return
if l1[0].id != "INST1:1:FLOW1:2:2104:15343:197391" or \
l2[0].id != "INST1:1:FLOW1:2:2104:15343:197391":
print("test_subst: fail (3)")
return
if str(l1[0].seq) != "CAGCCCTGGAGTTCCAC" or \
str(l2[0].seq) != "GTAGCTGAGATCGGAAG":
print("test_subst: fail (4)")
return
if l1[1].id != "INST1:1:FLOW1:2:2104:15343:197393" or \
l2[1].id != "INST1:1:FLOW1:2:2104:15343:197393":
print("test_subst: fail (5)")
return
if str(l1[1].seq) != "CANCCCTGGAGTTCCAC" or \
str(l2[1].seq) != "GTAGCTGAGATCGGAAG":
print("test_subst: fail (6)")
return
if os.path.exists("test_ind1_R1.fastq.gz") or \
os.path.exists("test_ind1_R2.fastq.gz"):
print("test_subst: fail (7)")
return
print("test_subst: pass")
def test_subst(self):
if self.verbose > 0:
print("launch test subst ...")