def make_output_folders(data_folder,
adapters_designed,
VERBOSE=0,
summary=True):
'''Make output folders for all adapters and unclassified (e.g. PhiX)'''
from hivwholeseq.utils.generic import mkdirs
# Make folders for the samples
for (adaID, s) in adapters_designed:
dirname = foldername_adapter(adaID)
mkdirs(data_folder + dirname)
if VERBOSE:
print 'Folder created:', dirname
# Make a default directory for unclassified reads
mkdirs(data_folder + 'unclassified_reads')
if VERBOSE:
print 'Folder created: unclassified reads'
if summary:
with open(get_demultiplex_summary_filename(data_folder), 'a') as f:
f.write('\n')
f.write(
'Folders created for samples and unclassified reads (including phix).'
)
f.write('\n')
def get_adapters_designed(dataset, VERBOSE=0, summary=True):
'''Get dict of the adapters designed for this experiment'''
adapters_designed = [(adaID, adapters_illumina[adaID])
for adaID in dataset['adapters']]
output = [['Designed adapters:'], ['adaID', 'seq', 'sample']]
for (adaID, s) in adapters_designed:
sample = dataset['samples'][dataset['adapters'].index(adaID)]
output.append([adaID, s, sample])
output = '\n'.join(map('\t'.join, output))
if VERBOSE:
print output
if summary:
with open(get_demultiplex_summary_filename(data_folder), 'a') as f:
f.write('\n')
f.write(output)
f.write('\n')
return adapters_designed
def get_adapters_designed(dataset, VERBOSE=0, summary=True):
'''Get dict of the adapters designed for this experiment'''
adapters_designed = [(adaID, adapters_illumina[adaID])
for adaID in dataset['adapters']]
output = [['Designed adapters:'],
['adaID', 'seq', 'sample']]
for (adaID, s) in adapters_designed:
sample = dataset['samples'][dataset['adapters'].index(adaID)]
output.append([adaID, s, sample])
output = '\n'.join(map('\t'.join, output))
if VERBOSE:
print output
if summary:
with open(get_demultiplex_summary_filename(data_folder), 'a') as f:
f.write('\n')
f.write(output)
f.write('\n')
return adapters_designed
def make_output_folders(data_folder, adapters_designed, VERBOSE=0, summary=True):
'''Make output folders for all adapters and unclassified (e.g. PhiX)'''
from hivwholeseq.utils.generic import mkdirs
# Make folders for the samples
for (adaID, s) in adapters_designed:
dirname = foldername_adapter(adaID)
mkdirs(data_folder+dirname)
if VERBOSE:
print 'Folder created:', dirname
# Make a default directory for unclassified reads
mkdirs(data_folder+'unclassified_reads')
if VERBOSE:
print 'Folder created: unclassified reads'
if summary:
with open(get_demultiplex_summary_filename(data_folder), 'a') as f:
f.write('\n')
f.write('Folders created for samples and unclassified reads (including phix).')
f.write('\n')
def demultiplex_reads_single_index(data_folder,
data_filenames,
adapters_designed,
maxreads=-1,
VERBOSE=0,
summary=True):
'''Demultiplex reads with single index adapters'''
# Get the read filenames
datafile_read1 = data_filenames['read1']
datafile_read2 = data_filenames['read2']
datafile_adapter = data_filenames['adapter']
# Open output files (compressed)
fouts = {
adaID: [
gzip.open(fn, 'wb', compresslevel=9)
for fn in get_read_filenames(data_folder, adaID, gzip=True)
]
for adaID, _ in adapters_designed
}
fouts['unclassified'] = [
gzip.open(fn, 'wb', compresslevel=9)
for fn in get_unclassified_reads_filenames(data_folder, gzip=True)
]
adapters_designed_inv = dict(map(reversed, adapters_designed))
adapters_strings = map(itemgetter(1), adapters_designed)
# Make sure you close the files
try:
# Iterate over all reads (using fast iterators)
with gzip.open(datafile_read1, 'rb') as fh1,\
gzip.open(datafile_read2, 'rb') as fh2,\
gzip.open(datafile_adapter, 'rb') as fha:
if VERBOSE >= 3:
print 'adaID'
print '--------------------'
adapters_found = Counter()
for i, (read1, read2, adapter) in enumerate(
izip(FGI(fh1), FGI(fh2), SeqIO.parse(fha, 'fastq'))):
if i == maxreads:
if VERBOSE:
print 'Maxreads reached.'
break
# Print some output
if VERBOSE and (not ((i + 1) % 10000)):
print i + 1
# If the adapter is not known, add it to the list
adapter_string = str(adapter.seq)
adapters_found[adapter_string] += 1
# If the adapter does not match any know one,
# throw into wastebin folder
if adapter_string not in adapters_strings:
adaID = 'unclassified'
else:
adaID = adapters_designed_inv[adapter_string]
if VERBOSE >= 3:
print adaID
# Write sequences (append to file, manual but fast)
fouts[adaID][0].write("@%s\n%s\n+\n%s\n" % read1)
fouts[adaID][1].write("@%s\n%s\n+\n%s\n" % read2)
if adapter_string not in adapters_strings:
SeqIO.write(adapter, fouts['unclassified'][2], 'fastq')
finally:
# Close all adaIDs
for fout in fouts.itervalues():
# Close both read 1 and read 2 (and barcode for unclassified)
for fou in fout:
fou.close()
if summary:
with open(get_demultiplex_summary_filename(data_folder), 'a') as f:
f.write('\n')
f.write('Total number of reads demultiplexed: ' + str(i + 1) +
'\n')
f.write('Adapters found across all reads:\n')
for e in adapters_found.most_common():
f.write('\t'.join(map(str, e)) + '\n')
def demultiplex_reads_dual_index(data_folder,
data_filenames,
adapters_designed,
maxreads=-1,
VERBOSE=0,
summary=True):
'''Demultiplex reads with dual index adapters'''
#FIXME: use gzipped files
# Get the read filenames
datafile_read1 = data_filenames['read1']
datafile_read2 = data_filenames['read2']
datafile_adapter1 = data_filenames['adapter1']
datafile_adapter2 = data_filenames['adapter2']
# Open output files
fouts = {
adaID:
(open(data_folder + foldername_adapter(adaID) + 'read1.fastq', 'w'),
open(data_folder + foldername_adapter(adaID) + 'read2.fastq', 'w'))
for adaID, _ in adapters_designed
}
fouts['unclassified'] = (
open(data_folder + 'unclassified_reads/read1.fastq', 'w'),
open(data_folder + 'unclassified_reads/read2.fastq', 'w'),
open(data_folder + 'unclassified_reads/adapter1.fastq', 'w'),
open(data_folder + 'unclassified_reads/adapter2.fastq', 'w'),
)
adapters_designed_inv = dict(map(reversed, adapters_designed))
adapters_strings = map(itemgetter(1), adapters_designed)
# Make sure you close the files
try:
# Iterate over all reads (using fast iterators)
with open(datafile_read1, 'r') as fh1,\
open(datafile_read2, 'r') as fh2,\
open(datafile_adapter1, 'r') as fha1,\
open(datafile_adapter2, 'r') as fha2:
if VERBOSE >= 3:
print 'adaID'
print '--------------------'
adapters_found = Counter()
for i, (read1, read2, adapter1, adapter2) in enumerate(
izip(FGI(fh1), FGI(fh2), SeqIO.parse(fha1, 'fastq'),
SeqIO.parse(fha2, 'fastq'))):
# Stop at the maximal number of reads (for testing)
if i == maxreads:
if VERBOSE:
print 'Maximal number of read pairs reached:', maxreads
break
if VERBOSE and (not ((i + 1) % 10000)):
print i + 1
# If the adapter is not known, add it to the list
adapter_string = '-'.join(
map(str, [adapter1.seq, adapter2.seq]))
adapters_found[adapter_string] += 1
# If the adapter does not match any know one,
# throw into wastebin folder
if adapter_string not in adapters_strings:
adaID = 'unclassified'
else:
adaID = adapters_designed_inv[adapter_string]
if VERBOSE >= 3:
print adaID
# Write sequences (append to file, manual but fast)
fouts[adaID][0].write("@%s\n%s\n+\n%s\n" % read1)
fouts[adaID][1].write("@%s\n%s\n+\n%s\n" % read2)
if adapter_string not in adapters_strings:
SeqIO.write(adapter1, fouts['unclassified'][2], 'fastq')
SeqIO.write(adapter2, fouts['unclassified'][3], 'fastq')
finally:
# Close all adaIDs
for fout in fouts.itervalues():
# Close both read 1 and read 2 (and barcode for unclassified)
for fou in fout:
fou.close()
if summary:
with open(get_demultiplex_summary_filename(data_folder), 'a') as f:
f.write('\n')
f.write('Adapters found across all reads:\n')
for e in adapters_found.most_common():
f.write('\t'.join(map(str, e)) + '\n')
VERBOSE = args.verbose
maxreads = args.maxreads
submit = args.submit
summary = args.summary
# If submit, outsource to the cluster
if submit:
fork_self(seq_run, VERBOSE=VERBOSE, maxreads=maxreads, summary=summary)
sys.exit()
# Specify the dataset
dataset = MiSeq_runs[seq_run]
data_folder = dataset['folder']
if summary:
with open(get_demultiplex_summary_filename(data_folder), 'w') as f:
f.write('Call: python demultiplex.py --run ' + seq_run +
' --verbose ' + str(VERBOSE) + '\n')
adapters_designed = get_adapters_designed(dataset,
VERBOSE=VERBOSE,
summary=summary)
make_output_folders(data_folder,
adapters_designed,
VERBOSE=VERBOSE,
summary=summary)
data_filenames = get_raw_read_files(dataset)
# Is it a dual index library?
def demultiplex_reads_single_index(data_folder, data_filenames, adapters_designed,
maxreads=-1, VERBOSE=0, summary=True):
'''Demultiplex reads with single index adapters'''
# Get the read filenames
datafile_read1 = data_filenames['read1']
datafile_read2 = data_filenames['read2']
datafile_adapter = data_filenames['adapter']
# Open output files (compressed)
fouts = {adaID: [gzip.open(fn, 'wb', compresslevel=9)
for fn in get_read_filenames(data_folder, adaID, gzip=True)]
for adaID, _ in adapters_designed}
fouts['unclassified'] = [gzip.open(fn, 'wb', compresslevel=9)
for fn in get_unclassified_reads_filenames(data_folder, gzip=True)]
adapters_designed_inv = dict(map(reversed, adapters_designed))
adapters_strings = map(itemgetter(1), adapters_designed)
# Make sure you close the files
try:
# Iterate over all reads (using fast iterators)
with gzip.open(datafile_read1, 'rb') as fh1,\
gzip.open(datafile_read2, 'rb') as fh2,\
gzip.open(datafile_adapter, 'rb') as fha:
if VERBOSE >= 3:
print 'adaID'
print '--------------------'
adapters_found = Counter()
for i, (read1, read2, adapter) in enumerate(izip(FGI(fh1), FGI(fh2),
SeqIO.parse(fha, 'fastq'))):
if i == maxreads:
if VERBOSE:
print 'Maxreads reached.'
break
# Print some output
if VERBOSE and (not ((i + 1) % 10000)):
print i + 1
# If the adapter is not known, add it to the list
adapter_string = str(adapter.seq)
adapters_found[adapter_string] += 1
# If the adapter does not match any know one,
# throw into wastebin folder
if adapter_string not in adapters_strings:
adaID = 'unclassified'
else:
adaID = adapters_designed_inv[adapter_string]
if VERBOSE >= 3:
print adaID
# Write sequences (append to file, manual but fast)
fouts[adaID][0].write("@%s\n%s\n+\n%s\n" % read1)
fouts[adaID][1].write("@%s\n%s\n+\n%s\n" % read2)
if adapter_string not in adapters_strings:
SeqIO.write(adapter, fouts['unclassified'][2], 'fastq')
finally:
# Close all adaIDs
for fout in fouts.itervalues():
# Close both read 1 and read 2 (and barcode for unclassified)
for fou in fout:
fou.close()
if summary:
with open(get_demultiplex_summary_filename(data_folder), 'a') as f:
f.write('\n')
f.write('Total number of reads demultiplexed: '+str(i+1)+'\n')
f.write('Adapters found across all reads:\n')
for e in adapters_found.most_common():
f.write('\t'.join(map(str, e))+'\n')
def demultiplex_reads_dual_index(data_folder, data_filenames, adapters_designed,
maxreads=-1, VERBOSE=0, summary=True):
'''Demultiplex reads with dual index adapters'''
#FIXME: use gzipped files
# Get the read filenames
datafile_read1 = data_filenames['read1']
datafile_read2 = data_filenames['read2']
datafile_adapter1 = data_filenames['adapter1']
datafile_adapter2 = data_filenames['adapter2']
# Open output files
fouts = {adaID: (open(data_folder+foldername_adapter(adaID)+'read1.fastq', 'w'),
open(data_folder+foldername_adapter(adaID)+'read2.fastq', 'w'))
for adaID, _ in adapters_designed}
fouts['unclassified'] = (open(data_folder+'unclassified_reads/read1.fastq', 'w'),
open(data_folder+'unclassified_reads/read2.fastq', 'w'),
open(data_folder+'unclassified_reads/adapter1.fastq', 'w'),
open(data_folder+'unclassified_reads/adapter2.fastq', 'w'),
)
adapters_designed_inv = dict(map(reversed, adapters_designed))
adapters_strings = map(itemgetter(1), adapters_designed)
# Make sure you close the files
try:
# Iterate over all reads (using fast iterators)
with open(datafile_read1, 'r') as fh1,\
open(datafile_read2, 'r') as fh2,\
open(datafile_adapter1, 'r') as fha1,\
open(datafile_adapter2, 'r') as fha2:
if VERBOSE >= 3:
print 'adaID'
print '--------------------'
adapters_found = Counter()
for i, (read1, read2,
adapter1,
adapter2) in enumerate(izip(FGI(fh1), FGI(fh2),
SeqIO.parse(fha1, 'fastq'),
SeqIO.parse(fha2, 'fastq'))):
# Stop at the maximal number of reads (for testing)
if i == maxreads:
if VERBOSE:
print 'Maximal number of read pairs reached:', maxreads
break
if VERBOSE and (not ((i + 1) % 10000)):
print i + 1
# If the adapter is not known, add it to the list
adapter_string = '-'.join(map(str, [adapter1.seq, adapter2.seq]))
adapters_found[adapter_string] += 1
# If the adapter does not match any know one,
# throw into wastebin folder
if adapter_string not in adapters_strings:
adaID = 'unclassified'
else:
adaID = adapters_designed_inv[adapter_string]
if VERBOSE >= 3:
print adaID
# Write sequences (append to file, manual but fast)
fouts[adaID][0].write("@%s\n%s\n+\n%s\n" % read1)
fouts[adaID][1].write("@%s\n%s\n+\n%s\n" % read2)
if adapter_string not in adapters_strings:
SeqIO.write(adapter1, fouts['unclassified'][2], 'fastq')
SeqIO.write(adapter2, fouts['unclassified'][3], 'fastq')
finally:
# Close all adaIDs
for fout in fouts.itervalues():
# Close both read 1 and read 2 (and barcode for unclassified)
for fou in fout:
fou.close()
if summary:
with open(get_demultiplex_summary_filename(data_folder), 'a') as f:
f.write('\n')
f.write('Adapters found across all reads:\n')
for e in adapters_found.most_common():
f.write('\t'.join(map(str, e))+'\n')
VERBOSE = args.verbose
maxreads = args.maxreads
submit = args.submit
summary = args.summary
# If submit, outsource to the cluster
if submit:
fork_self(seq_run, VERBOSE=VERBOSE, maxreads=maxreads, summary=summary)
sys.exit()
# Specify the dataset
dataset = MiSeq_runs[seq_run]
data_folder = dataset['folder']
if summary:
with open(get_demultiplex_summary_filename(data_folder), 'w') as f:
f.write('Call: python demultiplex.py --run '+seq_run+' --verbose '+str(VERBOSE)+'\n')
adapters_designed = get_adapters_designed(dataset, VERBOSE=VERBOSE, summary=summary)
make_output_folders(data_folder, adapters_designed, VERBOSE=VERBOSE,
summary=summary)
data_filenames = get_raw_read_files(dataset)
# Is it a dual index library?
if '-' not in adapters_designed[0][0]:
demultiplex_reads_single_index(data_folder, data_filenames, adapters_designed,
maxreads=maxreads, VERBOSE=VERBOSE,
summary=summary)
else:
