def test_fasta_reader_cleanup():
i_path = _data_path("fasta_reader_1.fasta")
fh = open(i_path)
with _new_argv([fh]):
reader = fastaReader(fh)
for _ in reader:
pass
assert (fh.closed)
def main():
# Read command line arguments
fasta_filename = sys.argv[1]
fasta_type = sys.argv[
2] or 'fasta' # should always be fasta or csfasta? what if txt?
qual_filename = sys.argv[3]
qual_type = sys.argv[4] or 'qualsanger' # qual454 qualsolid
output_filename = sys.argv[5]
force_quality_encoding = sys.argv[6]
if force_quality_encoding == 'None':
force_quality_encoding = None
format = 'sanger'
if fasta_type == 'csfasta' or qual_type == 'qualsolid':
format = 'cssanger'
elif qual_type == 'qualsolexa':
format = 'solexa'
elif qual_type == 'qualillumina':
format = 'illumina'
out = fastqWriter(path=output_filename,
format=format,
force_quality_encoding=force_quality_encoding)
if qual_filename == 'None':
qual_input = fastqFakeFastaScoreReader(
format, quality_encoding=force_quality_encoding)
else:
qual_input = fastaNamedReader(open(qual_filename, 'rt'))
fastq_combiner = fastqCombiner(format)
i = None
skip_count = 0
for i, sequence in enumerate(fastaReader(open(fasta_filename, 'rt'))):
quality = qual_input.get(sequence)
if quality:
fastq_read = fastq_combiner.combine(sequence, quality)
out.write(fastq_read)
else:
skip_count += 1
out.close()
if i is None:
print("Your file contains no valid FASTA sequences.")
else:
print(qual_input.has_data())
print('Combined %s of %s sequences with quality scores (%.2f%%).' %
(i - skip_count + 1, i + 1,
float(i - skip_count + 1) / float(i + 1) * 100.0))
def load_primers_as_re(primer_fasta, mm, rc=False):
#Read primer file and record all specified sequences
primers = set()
in_handle = open(primer_fasta, "rU")
reader = fastaReader(in_handle)
count = 0
for record in reader:
if rc:
seq = reverse_complement(record.sequence)
else:
seq = record.sequence
#primers.add(re.compile(make_reg_ex(seq)))
count += 1
for pattern in make_reg_ex_mm(seq, mm):
primers.add(pattern)
in_handle.close()
#Use set to avoid duplicates, sort to have longest first
#(so more specific primers found before less specific ones)
primers = sorted(set(primers), key=lambda p: -len(p))
return count, re.compile("|".join(primers)) #make one monster re!
def load_primers_as_re(primer_fasta, mm, rc=False):
#Read primer file and record all specified sequences
primers = set()
in_handle = open(primer_fasta, "rU")
reader = fastaReader(in_handle)
count = 0
for record in reader:
if rc:
seq = reverse_complement(record.sequence)
else:
seq = record.sequence
#primers.add(re.compile(make_reg_ex(seq)))
count += 1
for pattern in make_reg_ex_mm(seq, mm):
primers.add(pattern)
in_handle.close()
#Use set to avoid duplicates, sort to have longest first
#(so more specific primers found before less specific ones)
primers = sorted(set(primers), key=lambda p: -len(p))
return count, re.compile("|".join(primers)) #make one monster re!
def main():
#Read command line arguments
fasta_filename = sys.argv[1]
fasta_type = sys.argv[2] or 'fasta' #should always be fasta or csfasta? what if txt?
qual_filename = sys.argv[3]
qual_type = sys.argv[4] or 'qualsanger' #qual454 qualsolid
output_filename = sys.argv[5]
force_quality_encoding = sys.argv[6]
if force_quality_encoding == 'None':
force_quality_encoding = None
format = 'sanger'
if fasta_type == 'csfasta' or qual_type == 'qualsolid':
format = 'cssanger'
elif qual_type == 'qualsolexa':
format = 'solexa'
elif qual_type == 'qualillumina':
format = 'illumina'
out = fastqWriter( open( output_filename, 'wb' ), format = format, force_quality_encoding = force_quality_encoding )
if qual_filename == 'None':
qual_input = fastqFakeFastaScoreReader( format, quality_encoding = force_quality_encoding )
else:
qual_input = fastaNamedReader( open( qual_filename, 'rb' ) )
fastq_combiner = fastqCombiner( format )
i = None
skip_count = 0
for i, sequence in enumerate( fastaReader( open( fasta_filename, 'rb' ) ) ):
quality = qual_input.get( sequence )
if quality:
fastq_read = fastq_combiner.combine( sequence, quality )
out.write( fastq_read )
else:
skip_count += 1
out.close()
if i is None:
print "Your file contains no valid FASTA sequences."
else:
print qual_input.has_data()
print 'Combined %s of %s sequences with quality scores (%.2f%%).' % ( i - skip_count + 1, i + 1, float( i - skip_count + 1 ) / float( i + 1 ) * 100.0 )
if len(record.sequence) >= min_len:
record.quality = record.quality[:cut]
clipped += 1
writer.write(record)
else:
short_clipped += 1
elif keep_negatives:
if len(record) >= min_len:
negs += 1
writer.write(record)
else:
short_negs += 1
elif seq_format.lower() == "fasta":
in_handle = open(in_file, "rU")
out_handle = open(out_file, "w")
reader = fastaReader(in_handle)
writer = fastaWriter(out_handle)
#Following code is identical to that for FASTQ but without editing qualities
if forward:
for record in reader:
seq = record.sequence.upper()
result = primer.search(seq)
if result:
#Forward primer, take everything after it
cut = result.end()
record.sequence = seq[cut:]
if len(record.sequence) >= min_len:
clipped += 1
writer.write(record)
else:
short_clipped += 1
try:
manifest = ReadRocheXmlManifest(in_handle)
except ValueError:
manifest = None
out_handle = open(out_file, "wb")
writer = SffWriter(out_handle, xml=manifest)
in_handle.seek(0) #start again after getting manifest
count = writer.write_file(rename_seqrecords(SffIterator(in_handle), rename))
out_handle.close()
in_handle.close()
else:
#Use Galaxy for FASTA, QUAL or FASTQ
if seq_format.lower() in ["fasta", "csfasta"] \
or seq_format.lower().startswith("qual"):
from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
reader = fastaReader(open(in_file, "rU"))
writer = fastaWriter(open(out_file, "w"))
marker = ">"
elif seq_format.lower().startswith("fastq"):
from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
reader = fastqReader(open(in_file, "rU"))
writer = fastqWriter(open(out_file, "w"))
marker = "@"
else:
sys.exit("Unsupported file type %r" % seq_format)
#Now do the renaming
count = 0
renamed = 0
for record in reader:
#The [1:] is because the fastaReader leaves the > on the identifier,
#likewise the fastqReader leaves the @ on the identifier
if len(record.sequence) >= min_len:
record.quality = record.quality[:cut]
clipped += 1
writer.write(record)
else:
short_clipped += 1
elif keep_negatives:
if len(record) >= min_len:
negs += 1
writer.write(record)
else:
short_neg += 1
elif seq_format.lower()=="fasta":
in_handle = open(in_file, "rU")
out_handle = open(out_file, "w")
reader = fastaReader(in_handle)
writer = fastaWriter(out_handle)
#Following code is identical to that for FASTQ but without editing qualities
if forward:
for record in reader:
seq = record.sequence.upper()
result = primer.search(seq)
if result:
#Forward primer, take everything after it
cut = result.end()
record.sequence = seq[cut:]
if len(record.sequence) >= min_len:
clipped += 1
writer.write(record)
else:
short_clipped += 1
except ValueError:
manifest = None
out_handle = open(out_file, "wb")
writer = SffWriter(out_handle, xml=manifest)
in_handle.seek(0) # start again after getting manifest
count = writer.write_file(rename_seqrecords(SffIterator(in_handle), rename))
out_handle.close()
in_handle.close()
else:
# Use Galaxy for FASTA, QUAL or FASTQ
if seq_format.lower() in ["fasta", "csfasta"] or seq_format.lower().startswith(
"qual"
):
from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
reader = fastaReader(open(in_file, "rU"))
writer = fastaWriter(open(out_file, "w"))
marker = ">"
elif seq_format.lower().startswith("fastq"):
from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
reader = fastqReader(open(in_file, "rU"))
writer = fastqWriter(open(out_file, "w"))
marker = "@"
else:
sys.exit("Unsupported file type %r" % seq_format)
# Now do the renaming
count = 0
renamed = 0
for record in reader:
# The [1:] is because the fastaReader leaves the > on the identifier,