def trim_reads(data_folder,
adaID,
VERBOSE=0,
summary=True,
quality=25,
blocksize=10,
minlen_read1=100,
minlen_read2=50):
'''Trim low quality at the end of reads'''
fn_in = get_read_filenames(data_folder, adaID, gzip=True)
fn_out = get_read_filenames(data_folder, adaID, gzip=True, trimmed=True)
n_good = 0
n_discarded = 0
with gzip.open(fn_in[0], 'rb') as fin1, \
gzip.open(fn_in[1], 'rb') as fin2, \
gzip.open(fn_out[0], 'rb') as fout1, \
gzip.open(fn_out[1], 'wb') as fout2:
it1 = SeqIO.read(fin1, 'fastq')
it2 = SeqIO.read(fin2, 'fastq')
for irp, reads in enumerate(izip(it1, it2)):
if VERBOSE >= 2:
if not ((irp + 1) % 10000):
print irp + 1
# Trim both reads
trims = [
trim_read(read, quality=quality, blocksize=blocksize)
for read in reads
]
lrs = map(len, trims)
if (lrs[0] > minlen_read1) and (lrs[1] > minlen_read2):
SeqIO.write(trims[0], fout1, 'fastq')
SeqIO.write(trims[1], fout2, 'fastq')
n_good += 1
else:
n_discarded += 1
if VERBOSE:
print 'Trim lowq ends of reads:'
print 'Good:', n_good
print 'Discarded:', n_discarded
# Write summary to file
if summary:
with open(get_trim_summary_filename(data_folder, adaID), 'a') as f:
f.write('\n')
f.write('Trim low quality ends results: adaID ' + adaID + '\n')
f.write('Total:\t\t' + str(irp) + '\n')
f.write('Good:\t\t' + str(n_good) + '\n')
f.write('Discarded:\t' + str(n_discarded) + '\n')
def trim_reads(data_folder, adaID, VERBOSE=0, summary=True, quality=25, blocksize=10,
minlen_read1=100, minlen_read2=50):
'''Trim low quality at the end of reads'''
fn_in = get_read_filenames(data_folder, adaID, gzip=True)
fn_out = get_read_filenames(data_folder, adaID, gzip=True, trimmed=True)
n_good = 0
n_discarded = 0
with gzip.open(fn_in[0], 'rb') as fin1, \
gzip.open(fn_in[1], 'rb') as fin2, \
gzip.open(fn_out[0], 'rb') as fout1, \
gzip.open(fn_out[1], 'wb') as fout2:
it1 = SeqIO.read(fin1, 'fastq')
it2 = SeqIO.read(fin2, 'fastq')
for irp, reads in enumerate(izip(it1, it2)):
if VERBOSE >= 2:
if not ((irp + 1) % 10000):
print irp + 1
# Trim both reads
trims = [trim_read(read, quality=quality, blocksize=blocksize)
for read in reads]
lrs = map(len, trims)
if (lrs[0] > minlen_read1) and (lrs[1] > minlen_read2):
SeqIO.write(trims[0], fout1, 'fastq')
SeqIO.write(trims[1], fout2, 'fastq')
n_good += 1
else:
n_discarded += 1
if VERBOSE:
print 'Trim lowq ends of reads:'
print 'Good:', n_good
print 'Discarded:', n_discarded
# Write summary to file
if summary:
with open(get_trim_summary_filename(data_folder, adaID), 'a') as f:
f.write('\n')
f.write('Trim low quality ends results: adaID '+adaID+'\n')
f.write('Total:\t\t'+str(irp)+'\n')
f.write('Good:\t\t'+str(n_good)+'\n')
f.write('Discarded:\t'+str(n_discarded)+'\n')
# Specify the dataset
dataset = load_sequencing_run(seq_run)
data_folder = dataset.folder
# If the script is called with no adaID, iterate over all
samples = dataset.samples
if adaIDs is not None:
samples = samples.loc[samples.adapter.isin(adaIDs)]
if VERBOSE >= 2:
print samples.index.tolist()
# Iterate over all adaIDs
for samplename, sample in samples.iterrows():
adaID = str(sample.adapter)
# Submit to the cluster self if requested
if submit:
fork_self(seq_run, adaID, VERBOSE=VERBOSE, threads=threads,
reference=refname, summary=summary)
continue
if summary:
with open(get_trim_summary_filename(data_folder, adaID), 'w') as f:
f.write('Call: python trim_reads_lowq.py --run '+seq_run+\
' --adaIDs '+adaID+\
' --threads '+str(threads)+\
' --reference '+refname+\
' --verbose '+str(VERBOSE)+'\n')
trim_reads(data_folder, adaID, VERBOSE=VERBOSE, summary=summary)
# If the script is called with no adaID, iterate over all
samples = dataset.samples
if adaIDs is not None:
samples = samples.loc[samples.adapter.isin(adaIDs)]
if VERBOSE >= 2:
print samples.index.tolist()
# Iterate over all adaIDs
for samplename, sample in samples.iterrows():
adaID = str(sample.adapter)
# Submit to the cluster self if requested
if submit:
fork_self(seq_run,
adaID,
VERBOSE=VERBOSE,
threads=threads,
reference=refname,
summary=summary)
continue
if summary:
with open(get_trim_summary_filename(data_folder, adaID), 'w') as f:
f.write('Call: python trim_reads_lowq.py --run '+seq_run+\
' --adaIDs '+adaID+\
' --threads '+str(threads)+\
' --reference '+refname+\
' --verbose '+str(VERBOSE)+'\n')
trim_reads(data_folder, adaID, VERBOSE=VERBOSE, summary=summary)
