def main():
input_filename = sys.argv[1]
input_type = sys.argv[2] or 'sanger'
mate1_filename = sys.argv[3]
mate2_filename = sys.argv[4]
single1_filename = sys.argv[5]
single2_filename = sys.argv[6]
type = input_type
input = fastqNamedReader(open(input_filename, 'rb'), format=type)
mate1_out = fastqWriter(open(mate1_filename, 'wb'), format=type)
mate2_out = fastqWriter(open(mate2_filename, 'wb'), format=type)
single1_out = fastqWriter(open(single1_filename, 'wb'), format=type)
single2_out = fastqWriter(open(single2_filename, 'wb'), format=type)
joiner = fastqJoiner(type)
i = None
skip_count = 0
found = {}
for i, read in enumerate(
fastqReader(open(input_filename, 'rb'), format=type)):
if read.identifier in found:
del found[read.identifier]
continue
mate1 = input.get(read.identifier)
mate2 = input.get(joiner.get_paired_identifier(mate1))
if mate2:
# This is a mate pair
found[mate2.identifier] = None
if joiner.is_first_mate(mate1):
mate1_out.write(mate1)
mate2_out.write(mate2)
else:
mate1_out.write(mate2)
mate2_out.write(mate1)
else:
# This is a single
skip_count += 1
if joiner.is_first_mate(mate1):
single1_out.write(mate1)
else:
single2_out.write(mate1)
if i is None:
print "Your input file contained no valid FASTQ sequences."
else:
if skip_count:
print 'There were %i reads with no mate.' % skip_count
print 'De-interlaced %s pairs of sequences.' % (
(i - skip_count + 1) / 2)
input.close()
mate1_out.close()
mate2_out.close()
single1_out.close()
single2_out.close()
def main():
#Read command line arguments
input1_filename = sys.argv[1]
input1_type = sys.argv[2] or 'sanger'
input2_filename = sys.argv[3]
input2_type = sys.argv[4] or 'sanger'
output_filename = sys.argv[5]
if input1_type != input2_type:
print "WARNING: You are trying to join files of two different types: %s and %s." % (
input1_type, input2_type)
input2 = fastqNamedReader(open(input2_filename, 'rb'), input2_type)
joiner = fastqJoiner(input1_type)
out = fastqWriter(open(output_filename, 'wb'), format=input1_type)
i = None
skip_count = 0
for i, fastq_read in enumerate(
fastqReader(open(input1_filename, 'rb'), format=input1_type)):
identifier = joiner.get_paired_identifier(fastq_read)
fastq_paired = input2.get(identifier)
if fastq_paired is None:
skip_count += 1
else:
out.write(joiner.join(fastq_read, fastq_paired))
out.close()
if i is None:
print "Your file contains no valid FASTQ reads."
else:
print input2.has_data()
print 'Joined %s of %s read pairs (%.2f%%).' % (
i - skip_count + 1, i + 1,
float(i - skip_count + 1) / float(i + 1) * 100.0)
def main():
#Read command line arguments
input1_filename = sys.argv[1]
input1_type = sys.argv[2] or 'sanger'
input2_filename = sys.argv[3]
input2_type = sys.argv[4] or 'sanger'
output_filename = sys.argv[5]
if input1_type != input2_type:
print "WARNING: You are trying to join files of two different types: %s and %s." % ( input1_type, input2_type )
input2 = fastqNamedReader( open( input2_filename, 'rb' ), input2_type )
joiner = fastqJoiner( input1_type )
out = fastqWriter( open( output_filename, 'wb' ), format = input1_type )
i = None
skip_count = 0
for i, fastq_read in enumerate( fastqReader( open( input1_filename, 'rb' ), format = input1_type ) ):
identifier = joiner.get_paired_identifier( fastq_read )
fastq_paired = input2.get( identifier )
if fastq_paired is None:
skip_count += 1
else:
out.write( joiner.join( fastq_read, fastq_paired ) )
out.close()
if i is None:
print "Your file contains no valid FASTQ reads."
else:
print input2.has_data()
print 'Joined %s of %s read pairs (%.2f%%).' % ( i - skip_count + 1, i + 1, float( i - skip_count + 1 ) / float( i + 1 ) * 100.0 )
def main():
input_filename = sys.argv[1]
input_type = sys.argv[2] or 'sanger'
mate1_filename = sys.argv[3]
mate2_filename = sys.argv[4]
single1_filename = sys.argv[5]
single2_filename = sys.argv[6]
type = input_type
input = fastqNamedReader(path=input_filename, format=type)
mate1_out = fastqWriter(path=mate1_filename, format=type)
mate2_out = fastqWriter(path=mate2_filename, format=type)
single1_out = fastqWriter(path=single1_filename, format=type)
single2_out = fastqWriter(path=single2_filename, format=type)
joiner = fastqJoiner(type)
i = None
skip_count = 0
found = {}
for i, read in enumerate(fastqReader(path=input_filename, format=type)):
if read.identifier in found:
del found[read.identifier]
continue
mate1 = input.get(read.identifier)
mate2 = input.get(joiner.get_paired_identifier(mate1))
if mate2:
# This is a mate pair
found[mate2.identifier] = None
if joiner.is_first_mate(mate1):
mate1_out.write(mate1)
mate2_out.write(mate2)
else:
mate1_out.write(mate2)
mate2_out.write(mate1)
else:
# This is a single
skip_count += 1
if joiner.is_first_mate(mate1):
single1_out.write(mate1)
else:
single2_out.write(mate1)
if i is None:
print("Your input file contained no valid FASTQ sequences.")
else:
if skip_count:
print('There were %i reads with no mate.' % skip_count)
print('De-interlaced %s pairs of sequences.' % ((i - skip_count + 1) / 2))
input.close()
mate1_out.close()
mate2_out.close()
single1_out.close()
single2_out.close()
def main():
input_filename = sys.argv[1]
input_type = sys.argv[2] or 'sanger'
mate1_filename = sys.argv[3]
mate2_filename = sys.argv[4]
single1_filename = sys.argv[5]
single2_filename = sys.argv[6]
type = input_type
joiner = fastqJoiner(type)
i = None
skip_count = 0
found = {}
mate1_out = fastqWriter(path=mate1_filename, format=type)
mate2_out = fastqWriter(path=mate2_filename, format=type)
single1_out = fastqWriter(path=single1_filename, format=type)
single2_out = fastqWriter(path=single2_filename, format=type)
reader1 = fastqNamedReader(path=input_filename, format=type)
reader2 = fastqReader(path=input_filename, format=type)
with mate1_out, mate2_out, single1_out, single2_out, reader1, reader2:
for i, read in enumerate(reader2):
if read.identifier in found:
del found[read.identifier]
continue
mate1 = reader1.get(read.identifier)
mate2 = reader1.get(joiner.get_paired_identifier(mate1))
if mate2:
# This is a mate pair
found[mate2.identifier] = None
if joiner.is_first_mate(mate1):
mate1_out.write(mate1)
mate2_out.write(mate2)
else:
mate1_out.write(mate2)
mate2_out.write(mate1)
else:
# This is a single
skip_count += 1
if joiner.is_first_mate(mate1):
single1_out.write(mate1)
else:
single2_out.write(mate1)
if i is None:
print("Your input file contained no valid FASTQ sequences.")
else:
if skip_count:
print('There were %i reads with no mate.' % skip_count)
print('De-interlaced %s pairs of sequences.' % ((i - skip_count + 1) / 2))
def main():
mate1_filename = sys.argv[1]
mate1_type = sys.argv[2] or 'sanger'
mate2_filename = sys.argv[3]
mate2_type = sys.argv[4] or 'sanger'
outfile_pairs = sys.argv[5]
outfile_singles = sys.argv[6]
if mate1_type != mate2_type:
print(
"WARNING: You are trying to interlace files of two different types: %s and %s."
% (mate1_type, mate2_type))
return
type = mate1_type
joiner = fastqJoiner(type)
nof_singles = 0
nof_pairs = 0
i = None
j = None
out_pairs = fastqWriter(path=outfile_pairs, format=type)
out_singles = fastqWriter(path=outfile_singles, format=type)
mate2_input = fastqNamedReader(path=mate2_filename, format=type)
mate1_input = fastqNamedReader(path=mate1_filename, format=type)
reader1 = fastqReader(path=mate1_filename, format=type)
reader2 = fastqReader(path=mate2_filename, format=type)
with out_pairs, out_singles, mate2_input, mate1_input, reader1, reader2:
# Pairs + singles present in mate1
for i, mate1 in enumerate(reader1):
mate2 = mate2_input.get(joiner.get_paired_identifier(mate1))
if mate2:
out_pairs.write(mate1)
out_pairs.write(mate2)
nof_pairs += 1
else:
out_singles.write(mate1)
nof_singles += 1
# Singles present in mate2
for j, mate2 in enumerate(reader2):
mate1 = mate1_input.get(joiner.get_paired_identifier(mate2))
if not mate1:
out_singles.write(mate2)
nof_singles += 1
if (i is None) and (j is None):
print("Your input files contained no valid FASTQ sequences.")
else:
print('There were %s single reads.' % (nof_singles))
print('Interlaced %s pairs of sequences.' % (nof_pairs))
def main():
mate1_filename = sys.argv[1]
mate1_type = sys.argv[2] or 'sanger'
mate2_filename = sys.argv[3]
mate2_type = sys.argv[4] or 'sanger'
outfile_pairs = sys.argv[5]
outfile_singles = sys.argv[6]
if mate1_type != mate2_type:
print "WARNING: You are trying to interlace files of two different types: %s and %s." % ( mate1_type, mate2_type )
return
type = mate1_type
joiner = fastqJoiner( type )
out_pairs = fastqWriter( open( outfile_pairs, 'wb' ), format = type )
out_singles = fastqWriter( open( outfile_singles, 'wb' ), format = type )
# Pairs + singles present in mate1
nof_singles = 0
nof_pairs = 0
mate2_input = fastqNamedReader( open( mate2_filename, 'rb' ), format = type )
i = None
for i, mate1 in enumerate( fastqReader( open( mate1_filename, 'rb' ), format = type ) ):
mate2 = mate2_input.get( joiner.get_paired_identifier( mate1 ) )
if mate2:
out_pairs.write( mate1 )
out_pairs.write( mate2 )
nof_pairs += 1
else:
out_singles.write( mate1 )
nof_singles += 1
# Singles present in mate2
mate1_input = fastqNamedReader( open( mate1_filename, 'rb' ), format = type )
j = None
for j, mate2 in enumerate( fastqReader( open( mate2_filename, 'rb' ), format = type ) ):
mate1 = mate1_input.get( joiner.get_paired_identifier( mate2 ) )
if not mate1:
out_singles.write( mate2 )
nof_singles += 1
if (i is None) and (j is None):
print "Your input files contained no valid FASTQ sequences."
else:
print 'There were %s single reads.' % ( nof_singles )
print 'Interlaced %s pairs of sequences.' % ( nof_pairs )
mate1_input.close()
mate2_input.close()
out_pairs.close()
out_singles.close()
def main():
# Read command line arguments
input1_filename = sys.argv[1]
input1_type = sys.argv[2] or 'sanger'
input2_filename = sys.argv[3]
input2_type = sys.argv[4] or 'sanger'
output_filename = sys.argv[5]
fastq_style = sys.argv[6] or 'old'
paste = sys.argv[7] or ''
# --
if input1_type != input2_type:
print(
"WARNING: You are trying to join files of two different types: %s and %s."
% (input1_type, input2_type))
if fastq_style == 'new':
sep = sniff_sep(input1_filename)
joiner = FastqJoiner(input1_type, sep=sep, paste=paste)
else:
joiner = fq.fastqJoiner(input1_type, paste=paste)
# --
i = None
skip_count = 0
writer = fq.fastqWriter(path=output_filename, format=input1_type)
reader1 = fq.fastqReader(path=input1_filename, format=input1_type)
reader2 = fq.fastqNamedReader(path=input2_filename, format=input2_type)
with writer, reader1, reader2:
for i, fastq_read in enumerate(reader1):
identifier = joiner.get_paired_identifier(fastq_read)
fastq_paired = reader2.get(identifier)
if fastq_paired is None:
skip_count += 1
else:
writer.write(joiner.join(fastq_read, fastq_paired))
# this indent is correct: we still need access to reader2
if i is None:
print("Your file contains no valid FASTQ reads.")
else:
print(reader2.has_data())
print('Joined %s of %s read pairs (%.2f%%).' %
(i - skip_count + 1, i + 1,
(i - skip_count + 1) / (i + 1) * 100.0))
def main():
# Read command line arguments
input1_filename = sys.argv[1]
input1_type = sys.argv[2] or 'sanger'
input2_filename = sys.argv[3]
input2_type = sys.argv[4] or 'sanger'
output_filename = sys.argv[5]
fastq_style = sys.argv[6] or 'old'
paste = sys.argv[7] or ''
# --
if input1_type != input2_type:
print("WARNING: You are trying to join files of two different types: %s and %s." % (input1_type, input2_type))
if fastq_style == 'new':
sep = sniff_sep(input1_filename)
joiner = FastqJoiner(input1_type, sep=sep, paste=paste)
else:
joiner = fq.fastqJoiner(input1_type, paste=paste)
# --
input2 = fq.fastqNamedReader(path=input2_filename, format=input2_type)
out = fq.fastqWriter(path=output_filename, format=input1_type)
i = None
skip_count = 0
for i, fastq_read in enumerate(fq.fastqReader(path=input1_filename, format=input1_type)):
identifier = joiner.get_paired_identifier(fastq_read)
fastq_paired = input2.get(identifier)
if fastq_paired is None:
skip_count += 1
else:
out.write(joiner.join(fastq_read, fastq_paired))
out.close()
if i is None:
print("Your file contains no valid FASTQ reads.")
else:
print(input2.has_data())
print('Joined %s of %s read pairs (%.2f%%).' % (i - skip_count + 1, i + 1, (i - skip_count + 1) / (i + 1) * 100.0))
