def parse_fastx_sam_parallel(fastx_infile, sam_infile):
""" Parse fastx and resulting sam file in parallel - generator yielding (name, seq, alignment_list) tuples.
The sam file may contain multiple alignments per read. Program checks that the readnames match.
"""
fastx_generator = basic_seq_utilities.name_seq_generator_from_fasta_fastq(fastx_infile)
sam_generator = iter(HTSeq.bundle_multiple_alignments(HTSeq.SAM_Reader(sam_infile)))
if_finished_fastx, if_finished_sam = False, False
while True:
try: name, seq = fastx_generator.next()
except StopIteration: if_finished_fastx = True
try: alns = sam_generator.next()
except StopIteration: if_finished_sam = True
# if both finished, good, we're doine
if if_finished_fastx and if_finished_sam:
raise StopIteration
# if one file was finished but the other wasn't, error!
elif if_finished_fastx or if_finished_sam:
raise DeepseqError("Parsing seq/aln files in parallel - inconsistent finished states! "
+"(If finished: %s %s, %s %s)"%(fastx_infile, if_finished_fastx, sam_infile, if_finished_sam))
# if all the files still contained data, yield it
else:
name = name.split()[0]
name2 = alns[0].read.name.split()[0]
if not name2 == name:
raise DeepseqError("Non-matching readnames between files! %s in %s, %s in %s"%(fastx_infile, name,
sam_infile, name2))
yield (name, seq, alns)
def trim_prefix(prefix_bases, infile, trimmed_outfile, wrong_prefix_outfile=os.devnull,
INFOFILE=None, verbosity=1):
""" Trim prefix_bases from seqs in infile and print to trimmed_outfile; print other seqs to wrong_prefix_outfile.
Reads fasta or fastq files; outputs fasta files only.
For each seq in infile, if seq starts with prefix_bases, trim them and print result to trimmed_outfile;
otherwise print full seq to wrong_prefix_outfile (if not None).
INFOFILE should be an open file handle to print summary info to, or None;
verbosity governs how much is printed to stdout
"""
text = "### Trimming %s from start of each sequence in %s (output to %s, untrimmed to %s)\n"%(prefix_bases, infile,
trimmed_outfile, wrong_prefix_outfile)
# MAYBE-TODO modify so it can output fastq too?
if INFOFILE is not None: INFOFILE.write(text+'\n')
if verbosity>0: print text
N_trimmed, N_untrimmed = 0, 0
with open(trimmed_outfile, 'w') as TRIMMED_OUTFILE:
with open(wrong_prefix_outfile, 'w') as WRONG_PREFIX_OUTFILE:
# MAYBE-TODO right now if wrong_prefix_outfile==None, /dev/null is used - it would be faster with a custom file-like object that doesn't touch the OS, but I'm not sure how to write one so it can be opened! See general_utilities.FAKE_OUTFILE for an already open one.
name_seq_generator = name_seq_generator_from_fasta_fastq(infile, verbosity>2)
for name,seq in name_seq_generator:
if_trimmed = _trim_prefix_single(name, seq, prefix_bases, TRIMMED_OUTFILE, WRONG_PREFIX_OUTFILE)
if if_trimmed: N_trimmed += 1
else: N_untrimmed += 1
N_total = N_trimmed + N_untrimmed
text = "Trimmed sequences: %s\nUntrimmed sequences: %s\n"%(value_and_percentages(N_trimmed, [N_total]),
value_and_percentages(N_untrimmed, [N_total]))
if INFOFILE is not None: INFOFILE.write(text+'\n')
if verbosity>1: print text
return N_trimmed, N_untrimmed
def trim_prefix(prefix_bases,
infile,
trimmed_outfile,
wrong_prefix_outfile=os.devnull,
INFOFILE=None,
verbosity=1):
""" Trim prefix_bases from seqs in infile and print to trimmed_outfile; print other seqs to wrong_prefix_outfile.
Reads fasta or fastq files; outputs fasta files only.
For each seq in infile, if seq starts with prefix_bases, trim them and print result to trimmed_outfile;
otherwise print full seq to wrong_prefix_outfile (if not None).
INFOFILE should be an open file handle to print summary info to, or None;
verbosity governs how much is printed to stdout
"""
text = "### Trimming %s from start of each sequence in %s (output to %s, untrimmed to %s)\n" % (
prefix_bases, infile, trimmed_outfile, wrong_prefix_outfile)
# MAYBE-TODO modify so it can output fastq too?
if INFOFILE is not None: INFOFILE.write(text + '\n')
if verbosity > 0: print text
N_trimmed, N_untrimmed = 0, 0
with open(trimmed_outfile, 'w') as TRIMMED_OUTFILE:
with open(wrong_prefix_outfile, 'w') as WRONG_PREFIX_OUTFILE:
# MAYBE-TODO right now if wrong_prefix_outfile==None, /dev/null is used - it would be faster with a custom file-like object that doesn't touch the OS, but I'm not sure how to write one so it can be opened! See general_utilities.FAKE_OUTFILE for an already open one.
name_seq_generator = name_seq_generator_from_fasta_fastq(
infile, verbosity > 2)
for name, seq in name_seq_generator:
if_trimmed = _trim_prefix_single(name, seq, prefix_bases,
TRIMMED_OUTFILE,
WRONG_PREFIX_OUTFILE)
if if_trimmed: N_trimmed += 1
else: N_untrimmed += 1
N_total = N_trimmed + N_untrimmed
text = "Trimmed sequences: %s\nUntrimmed sequences: %s\n" % (
value_and_percentages(N_trimmed, [N_total]),
value_and_percentages(N_untrimmed, [N_total]))
if INFOFILE is not None: INFOFILE.write(text + '\n')
if verbosity > 1: print text
return N_trimmed, N_untrimmed
