def getAvgLength(input):
AvgLength = []
for title, seq, qual in FastqGeneralIterator(open(input)):
AvgLength.append(len(seq))
Average = sum(AvgLength) / float(len(AvgLength))
Min = min(AvgLength)
Max = max(AvgLength)
a = np.array(AvgLength)
nintyfive = np.percentile(a, 5)
return (Average, Min, Max, int(nintyfive))
#remove logfile if exists
log_name = args.out + '.amptk-dada2.log'
if os.path.isfile(log_name):
amptklib.removefile(log_name)
amptklib.setupLogging(log_name)
FNULL = open(os.devnull, 'w')
cmd_args = " ".join(sys.argv) + '\n'
amptklib.log.debug(cmd_args)
print "-------------------------------------------------------"
#initialize script, log system info and usearch version
amptklib.SystemInfo()
#Do a version check
usearch = args.usearch
amptklib.versionDependencyChecks(usearch)
#check dependencies
programs = ['Rscript']
amptklib.CheckDependencies(programs)
lines = [line.rstrip('\n') for line in input]
remove = remove + lines
if args.list:
lines = args.list
remove = remove + lines
#make sure it is a set, faster lookup
keep_list = set(remove)
count = len(keep_list)
#now run filtering
keep_count = 0
total_count = 0
#rename to base
if args.out.endswith('.gz'):
outfile = args.out.replace('.gz', '')
else:
outfile = args.out
#run filtering
filter_sample(SeqIn, outfile)
#compress and clean
if args.out.endswith('.gz'): #compress in place
amptklib.Fzip_inplace(outfile)
if args.input.endswith('.gz'):
amptklib.removefile(SeqIn)
print("Removed %i samples" % count)
print("Kept %i reads out of %i total reads" % (keep_count, total_count))
)
#create OTU phylogeny for downstream processes
amptklib.log.info("Generating phylogenetic tree")
tree_out = base + '.tree.phy'
cmd = [usearch, '-cluster_agg', args.fasta, '-treeout', tree_out]
amptklib.runSubprocess(cmd, amptklib.log)
#print some summary file locations
amptklib.log.info("Taxonomy finished: %s" % taxFinal)
if args.otu_table and not args.method == 'blast':
amptklib.log.info("Classic OTU table with taxonomy: %s" % taxTable)
#output final OTU table in Biom v1.0 (i.e. json format if biom installed)
outBiom = base + '.biom'
if amptklib.which('biom'):
amptklib.removefile(outBiom)
cmd = [
'biom', 'convert', '-i', tmpTable, '-o', outBiom + '.tmp',
'--table-type', "OTU table", '--to-json'
]
amptklib.runSubprocess(cmd, amptklib.log)
if args.mapping_file:
cmd = [
'biom', 'add-metadata', '-i', outBiom + '.tmp', '-o', outBiom,
'--observation-metadata-fp', qiimeTax, '-m', args.mapping_file,
'--sc-separated', 'taxonomy', '--output-as-json'
]
amptklib.runSubprocess(cmd, amptklib.log)
else:
cmd = [
'biom', 'add-metadata', '-i', outBiom + '.tmp', '-o', outBiom,
parser.add_argument('-o','--out', help='Base output name')
parser.add_argument('--min_reads_otu', default=2, type=int, help='Minimum number of reads per OTU for experiment')
parser.add_argument('-u','--usearch', dest="usearch", default='usearch9', help='USEARCH9 EXE')
parser.add_argument('--debug', action='store_true', help='Remove Intermediate Files')
args=parser.parse_args()
if not args.out:
#get base name of files
base = args.otu_table.split(".otu_table")
base = base[0]
else:
base = args.out
#remove logfile if exists
log_name = base + '.amptk-filter.log'
amptklib.removefile(log_name)
amptklib.setupLogging(log_name)
FNULL = open(os.devnull, 'w')
cmd_args = " ".join(sys.argv)+'\n'
amptklib.log.debug(cmd_args)
print "-------------------------------------------------------"
#initialize script, log system info and usearch version
amptklib.SystemInfo()
#Do a version check
usearch = args.usearch
amptklib.versionDependencyChecks(usearch)
#check if otu_table is empty
amptklib.log.info("Loading OTU table: %s" % args.otu_table)
if k not in barcodes_found:
barcodes_found.append(k)
amptklib.log.info("Found %i barcoded samples\n%s" %
(len(BarcodeCount), barcode_counts))
if not args.mapping_file:
#create a generic mappingfile for downstream processes
genericmapfile = args.out + '.mapping_file.txt'
amptklib.CreateGenericMappingFile(barcode_file, FwdPrimer,
revcomp_lib.RevComp(RevPrimer), Adapter,
genericmapfile, barcodes_found)
#compress the output to save space
FinalDemux = catDemux + '.gz'
amptklib.Fzip(catDemux, FinalDemux, cpus)
amptklib.removefile(catDemux)
if gzip_list:
for file in gzip_list:
file = file.replace('.gz', '')
amptklib.removefile(file)
#get file size
filesize = os.path.getsize(FinalDemux)
readablesize = amptklib.convertSize(filesize)
amptklib.log.info("Output file: %s (%s)" % (FinalDemux, readablesize))
amptklib.log.info("Mapping file: %s" % genericmapfile)
print "-------------------------------------------------------"
if 'win32' in sys.platform:
print "\nExample of next cmd: amptk cluster -i %s -o out\n" % (FinalDemux)
else:
def primer2Strip(file, GoodOut, BadOut, fwdprimer, revprimer):
#now run primer strip
if args.reverse:
if not args.rev_primer:
print("ERROR: if reverse reads passed you must provide -r,--rev_primer")
sys.exit(1)
#first run forwards
GoodFor = args.out + '.fwd.stripped.fq'
BadFor = args.out + '.fwd.no_primer.fq'
primerStrip(args.input, GoodFor, BadFor, args.fwd_primer, args.rev_primer)
#now run reverse
GoodRev = args.out + '.rev.stripped.fq'
BadRev = args.out + '.rev.no_primer.fq'
primerStrip(args.reverse, GoodRev, BadRev, args.rev_primer, args.fwd_primer)
#now get bad reads into list
singleRev = []
singleFor = []
for title, seq, qual in FastqGeneralIterator(open(BadFor)):
singleRev.append(title.split(' ')[0])
for title, seq, qual in FastqGeneralIterator(open(BadRev)):
singleFor.append(title.split(' ')[0])
bothfail = sorted(set(singleRev) & set(singleFor), key = singleFor.index)
#now get PE and singletons
PEfor = args.out +'.pe_R1.fastq'
PErev = args.out +'.pe_R2.fastq'
SEfor = args.out +'.fwd.singletons.fastq'
SErev = args.out +'.rev.singletons.fastq'
with open(PEfor, 'w') as peF:
with open(SEfor, 'w') as seF:
for title, seq, qual in FastqGeneralIterator(open(GoodFor)):
ID = title.split(' ')[0]
if not ID in singleFor:
peF.write("@%s\n%s\n+\n%s\n" % (title, seq, qual))
else:
seF.write("@%s\n%s\n+\n%s\n" % (title, seq, qual))
with open(PErev, 'w') as peR:
with open(SErev, 'w') as seR:
for title, seq, qual in FastqGeneralIterator(open(GoodRev)):
ID = title.split(' ')[0]
if not ID in singleRev:
peR.write("@%s\n%s\n+\n%s\n" % (title, seq, qual))
else:
seR.write("@%s\n%s\n+\n%s\n" % (title, seq, qual))
#do some counts of output and cleanup
total = amptklib.countfastq(args.input)
passed = amptklib.countfastq(PEfor)
passedrev = amptklib.countfastq(PErev)
if passed != passedrev:
print("Error: forward reads %i != reverse reads %i" % (passed, passedrev))
nopaired = len(singleFor) + len(singleRev)
failed = len(bothfail)
print("%i total reads" % total)
print("%i primer found properly paired: %s, %s" % (passed, PEfor, PErev))
print("%i primer found singletons: %s, %s" % (nopaired, SEfor, SErev))
print("%i primer not found in either forward or reverse reads" % (failed))
amptklib.removefile(GoodFor)
amptklib.removefile(GoodRev)
else:
GoodOut = args.out +'.stripped.fq'
BadOut = args.out +'.no_primer_found.fq'
primerStrip(args.input, GoodOut, BadOut, args.fwd_primer, False)
total = amptklib.countfastq(args.input)
passed = amptklib.countfastq(GoodOut)
failed = amptklib.countfastq(BadOut)
print("%i total reads" % total)
print("%i primer found/stripped: %s" % (passed, GoodOut))
print("%i primer not found: %s" % (failed, BadOut))
seR.write("@%s\n%s\n+\n%s\n" % (title, seq, qual))
#do some counts of output and cleanup
total = amptklib.countfastq(args.input)
passed = amptklib.countfastq(PEfor)
passedrev = amptklib.countfastq(PErev)
if passed != passedrev:
print("Error: forward reads %i != reverse reads %i" %
(passed, passedrev))
nopaired = len(singleFor) + len(singleRev)
failed = len(bothfail)
print("-------------------------------------------------------")
print("%i total reads" % total)
print("%i primer found properly paired: %s, %s" % (passed, PEfor, PErev))
print("%i primer found singletons: %s, %s" % (nopaired, SEfor, SErev))
print("%i primer not found in either forward or reverse reads" % (failed))
amptklib.removefile(GoodFor)
amptklib.removefile(GoodRev)
else:
#setup tmpdir
tmpdir = args.out.split('.')[0] + '_' + str(os.getpid())
if not os.path.exists(tmpdir):
os.makedirs(tmpdir)
GoodOut = args.out + '.stripped.fq'
BadOut = args.out + '.no_primer_found.fq'
filelist = splitter(args.input, tmpdir)
amptklib.runMultiProgress(primerStrip, filelist, cpus)
combiner(tmpdir, ".good", GoodOut)
combiner(tmpdir, ".bad", BadOut)
shutil.rmtree(tmpdir)
total = amptklib.countfastq(args.input)
amptklib.runSubprocess(cmd, amptklib.log)
#count OTUs
otu_count = amptklib.countfasta(newOTUs)
amptklib.log.info('{0:,}'.format(otu_count) + ' OTUs remaining')
#count reads mapped
total = amptklib.line_count(uc_out)
orig_total = amptklib.countfasta(tmpReads)
amptklib.log.info('{0:,}'.format(total) + ' reads mapped to OTUs ' +
'({0:.0f}%)'.format(total / float(orig_total) * 100))
#Print location of files to STDOUT
print "-------------------------------------------------------"
print "Clustered OTUs: %s" % newOTUs
print "OTU Table: %s" % newTable
print "-------------------------------------------------------"
#cleanup
amptklib.removefile(tmpReads)
amptklib.removefile(uc_out)
otu_print = newOTUs.split('/')[-1]
tab_print = newTable.split('/')[-1]
if 'win32' in sys.platform:
print "\nExample of next cmd: amptk filter -i %s -f %s -b <mock barcode>\n" % (
tab_print, otu_print)
else:
print colr.WARN + "\nExample of next cmd:" + colr.END + " amptk filter -i %s -f %s -b <mock barcode>\n" % (
tab_print, otu_print)
for file in os.listdir(folder):
if file.endswith(".fq"):
file = os.path.join(folder, file)
file_list.append(file)
p = multiprocessing.Pool(cpus)
for f in file_list:
#worker(f)
p.apply_async(worker, [f])
p.close()
p.join()
#get filtered results
catDemux = args.out
with open(catDemux, 'w') as outfile:
for filename in glob.glob(os.path.join(folder,'*.filter.fq')):
if filename == catDemux:
continue
with open(filename, 'rU') as readfile:
shutil.copyfileobj(readfile, outfile)
if catDemux.endswith('.gz'):
amptklib.Fzip_inplace(catDemux)
shutil.rmtree(folder)
print "----------------------------------"
countBarcodes(args.out)
print "----------------------------------"
print "Script finished, output in %s" % args.out
if args.input.endswith('.gz'):
amptklib.removefile(tmpinput)
amptklib.log.info("Now Gzipping files")
for file in os.listdir(args.out):
if file.endswith(".fastq"):
file_path = os.path.join(args.out, file)
amptklib.Fzip_inplace(file_path)
#after all files demuxed into output folder, loop through and create SRA metadata file
filelist = []
for file in os.listdir(args.out):
if file.endswith(".fastq.gz"):
filelist.append(file)
amptklib.log.info("Finished: output in %s" % args.out)
#clean up if gzipped
if args.FASTQ.endswith('.gz'):
amptklib.removefile(FASTQ_IN)
#check for BioSample meta file
if args.biosample:
amptklib.log.info(
"NCBI BioSample file detected, creating SRA metadata file")
#load in BioSample file to dictionary
with open(args.biosample, 'rU') as input:
reader = csv.reader(input, delimiter='\t')
header = next(reader)
acc = header.index('Accession')
sample = header.index('Sample Name')
bio = header.index('BioProject')
try:
host = header.index('Host')
except ValueError:
ID = line.split("=", 1)[-1].split(";")[0]
if ID not in BarcodeCount:
BarcodeCount[ID] = 1
else:
BarcodeCount[ID] += 1
#now let's count the barcodes found and count the number of times they are found.
barcode_counts = "%30s: %s" % ('Sample', 'Count')
for k, v in natsorted(BarcodeCount.items(), key=lambda (k, v): v,
reverse=True):
barcode_counts += "\n%30s: %s" % (k, str(BarcodeCount[k]))
amptklib.log.info("Found %i barcoded samples\n%s" %
(len(BarcodeCount), barcode_counts))
#compress the output to save space
FinalDemux = Demux + '.gz'
amptklib.Fzip(Demux, FinalDemux, cpus)
amptklib.removefile(Demux)
#get file size
filesize = os.path.getsize(FinalDemux)
readablesize = amptklib.convertSize(filesize)
amptklib.log.info("Output file: %s (%s)" % (FinalDemux, readablesize))
amptklib.log.info("Mapping file: %s" % args.mapping_file)
print "-------------------------------------------------------"
if 'win32' in sys.platform:
print "\nExample of next cmd: amptk cluster -i %s -o out\n" % (FinalDemux)
else:
print col.WARN + "\nExample of next cmd: " + col.END + "amptk cluster -i %s -o out\n" % (
FinalDemux)
