def read_single_with_titles(filename, alphabet):
global title_to_ids
iterator = FastaIterator(open(filename), alphabet, title_to_ids)
record = iterator.next()
try:
second = iterator.next()
except StopIteration:
second = None
assert record is not None and second is None
return record
def read_single_with_titles(filename, alphabet):
global title_to_ids
iterator = FastaIterator(open(filename), alphabet, title_to_ids)
record = iterator.next()
try:
second = iterator.next()
except StopIteration:
second = None
assert record is not None and second is None
return record
def PairedFastaQualIterator(fasta_handle, qual_handle, alphabet = single_letter_alphabet, title2ids = None) :
"""Iterate over matched FASTA and QUAL files as SeqRecord objects.
For example, consider this short QUAL file::
>EAS54_6_R1_2_1_413_324
26 26 18 26 26 26 26 26 26 26 26 26 26 26 26 22 26 26 26 26
26 26 26 23 23
>EAS54_6_R1_2_1_540_792
26 26 26 26 26 26 26 26 26 26 26 22 26 26 26 26 26 12 26 26
26 18 26 23 18
>EAS54_6_R1_2_1_443_348
26 26 26 26 26 26 26 26 26 26 26 24 26 22 26 26 13 22 26 18
24 18 18 18 18
And a matching FASTA file::
>EAS54_6_R1_2_1_413_324
CCCTTCTTGTCTTCAGCGTTTCTCC
>EAS54_6_R1_2_1_540_792
TTGGCAGGCCAAGGCCGATGGATCA
>EAS54_6_R1_2_1_443_348
GTTGCTTCTGGCGTGGGTGGGGGGG
You can parse these separately using Bio.SeqIO with the "qual" and
"fasta" formats, but then you'll get a group of SeqRecord objects with
no sequence, and a matching group with the sequence but not the
qualities. Because it only deals with one input file handle, Bio.SeqIO
can't be used to read the two files together - but this function can!
For example,
>>> rec_iter = PairedFastaQualIterator(open("Quality/example.fasta", "rU"),
... open("Quality/example.qual", "rU"))
>>> for record in rec_iter :
... print record.id, record.seq
EAS54_6_R1_2_1_413_324 CCCTTCTTGTCTTCAGCGTTTCTCC
EAS54_6_R1_2_1_540_792 TTGGCAGGCCAAGGCCGATGGATCA
EAS54_6_R1_2_1_443_348 GTTGCTTCTGGCGTGGGTGGGGGGG
As with the FASTQ or QUAL parsers, if you want to look at the qualities,
they are in each record's per-letter-annotation dictionary as a simple
list of integers:
>>> print record.letter_annotations["phred_quality"]
[26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 24, 26, 22, 26, 26, 13, 22, 26, 18, 24, 18, 18, 18, 18]
If you have access to data as a FASTQ format file, using that directly
would be simpler and more straight forward. Note that you can easily use
this function to convert paired FASTA and QUAL files into FASTQ files:
>>> from Bio import SeqIO
>>> rec_iter = PairedFastaQualIterator(open("Quality/example.fasta", "rU"),
... open("Quality/example.qual", "rU"))
>>> out_handle = open("Quality/temp.fastq", "w")
>>> SeqIO.write(rec_iter, out_handle, "fastq")
3
>>> out_handle.close()
And don't forget to clean up the temp file if you don't need it anymore:
>>> import os
>>> os.remove("Quality/temp.fastq")
"""
from Bio.SeqIO.FastaIO import FastaIterator
fasta_iter = FastaIterator(fasta_handle, alphabet=alphabet, \
title2ids=title2ids)
qual_iter = QualPhredIterator(qual_handle, alphabet=alphabet, \
title2ids=title2ids)
#Using zip(...) would create a list loading everything into memory!
#It would also not catch any extra records found in only one file.
while True :
try :
f_rec = fasta_iter.next()
except StopIteration :
f_rec = None
try :
q_rec = qual_iter.next()
except StopIteration :
q_rec = None
if f_rec is None and q_rec is None :
#End of both files
break
if f_rec is None :
raise ValueError("FASTA file has more entries than the QUAL file.")
if q_rec is None :
raise ValueError("QUAL file has more entries than the FASTA file.")
if f_rec.id != q_rec.id :
raise ValueError("FASTA and QUAL entries do not match (%s vs %s)." \
% (f_rec.id, q_rec.id))
if len(f_rec) != len(q_rec.letter_annotations["phred_quality"]) :
raise ValueError("Sequence length and number of quality scores disagree for %s" \
% f_rec.id)
#Merge the data....
f_rec.letter_annotations["phred_quality"] = q_rec.letter_annotations["phred_quality"]
yield f_rec
def PairedFastaQualIterator(fasta_handle,
qual_handle,
alphabet=single_letter_alphabet,
title2ids=None):
"""Iterate over matched FASTA and QUAL files as SeqRecord objects.
For example, consider this short QUAL file::
>EAS54_6_R1_2_1_413_324
26 26 18 26 26 26 26 26 26 26 26 26 26 26 26 22 26 26 26 26
26 26 26 23 23
>EAS54_6_R1_2_1_540_792
26 26 26 26 26 26 26 26 26 26 26 22 26 26 26 26 26 12 26 26
26 18 26 23 18
>EAS54_6_R1_2_1_443_348
26 26 26 26 26 26 26 26 26 26 26 24 26 22 26 26 13 22 26 18
24 18 18 18 18
And a matching FASTA file::
>EAS54_6_R1_2_1_413_324
CCCTTCTTGTCTTCAGCGTTTCTCC
>EAS54_6_R1_2_1_540_792
TTGGCAGGCCAAGGCCGATGGATCA
>EAS54_6_R1_2_1_443_348
GTTGCTTCTGGCGTGGGTGGGGGGG
You can parse these separately using Bio.SeqIO with the "qual" and
"fasta" formats, but then you'll get a group of SeqRecord objects with
no sequence, and a matching group with the sequence but not the
qualities. Because it only deals with one input file handle, Bio.SeqIO
can't be used to read the two files together - but this function can!
For example,
>>> rec_iter = PairedFastaQualIterator(open("Quality/example.fasta", "rU"),
... open("Quality/example.qual", "rU"))
>>> for record in rec_iter :
... print record.id, record.seq
EAS54_6_R1_2_1_413_324 CCCTTCTTGTCTTCAGCGTTTCTCC
EAS54_6_R1_2_1_540_792 TTGGCAGGCCAAGGCCGATGGATCA
EAS54_6_R1_2_1_443_348 GTTGCTTCTGGCGTGGGTGGGGGGG
As with the FASTQ or QUAL parsers, if you want to look at the qualities,
they are in each record's per-letter-annotation dictionary as a simple
list of integers:
>>> print record.letter_annotations["phred_quality"]
[26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 24, 26, 22, 26, 26, 13, 22, 26, 18, 24, 18, 18, 18, 18]
If you have access to data as a FASTQ format file, using that directly
would be simpler and more straight forward. Note that you can easily use
this function to convert paired FASTA and QUAL files into FASTQ files:
>>> from Bio import SeqIO
>>> rec_iter = PairedFastaQualIterator(open("Quality/example.fasta", "rU"),
... open("Quality/example.qual", "rU"))
>>> out_handle = open("Quality/temp.fastq", "w")
>>> SeqIO.write(rec_iter, out_handle, "fastq")
3
>>> out_handle.close()
And don't forget to clean up the temp file if you don't need it anymore:
>>> import os
>>> os.remove("Quality/temp.fastq")
"""
from Bio.SeqIO.FastaIO import FastaIterator
fasta_iter = FastaIterator(fasta_handle, alphabet=alphabet, \
title2ids=title2ids)
qual_iter = QualPhredIterator(qual_handle, alphabet=alphabet, \
title2ids=title2ids)
#Using zip(...) would create a list loading everything into memory!
#It would also not catch any extra records found in only one file.
while True:
try:
f_rec = fasta_iter.next()
except StopIteration:
f_rec = None
try:
q_rec = qual_iter.next()
except StopIteration:
q_rec = None
if f_rec is None and q_rec is None:
#End of both files
break
if f_rec is None:
raise ValueError("FASTA file has more entries than the QUAL file.")
if q_rec is None:
raise ValueError("QUAL file has more entries than the FASTA file.")
if f_rec.id != q_rec.id:
raise ValueError("FASTA and QUAL entries do not match (%s vs %s)." \
% (f_rec.id, q_rec.id))
if len(f_rec) != len(q_rec.letter_annotations["phred_quality"]):
raise ValueError("Sequence length and number of quality scores disagree for %s" \
% f_rec.id)
#Merge the data....
f_rec.letter_annotations["phred_quality"] = q_rec.letter_annotations[
"phred_quality"]
yield f_rec
