cutadapt "succinct" patch

cutadapt.sufccinct.patch

diff -rupN '--exclude=.git' cutadapt/cutadapt/report.py cutadapt_patched/cutadapt/report.py
--- cutadapt/cutadapt/report.py	2015-03-26 13:00:26.163894349 -0500
+++ cutadapt_patched/cutadapt/report.py	2015-03-26 12:58:56.944023106 -0500
@@ -252,3 +252,55 @@ def print_statistics(adapters_pair, pair
 		print('    Please see the detailed output above.')
 
 	sys.stdout = old_stdout
+
+def print_succinct(adapters_pair, paired, stats,
+		modifiers, modifiers2, writers, file=None):
+	"""Print single-line summary"""
+	old_stdout = sys.stdout
+	if file is not None:
+		sys.stdout = file
+	n = stats.n
+
+	too_short = 0
+	too_long = 0
+	written = 0
+	written_bp = 0
+	too_many_n = 0
+	for w in writers:
+		if isinstance(w, TooShortReadFilter):
+			too_short = w.too_short
+		elif isinstance(w, TooLongReadFilter):
+			too_long = w.too_long
+		elif isinstance(w, NContentTrimmer):
+			too_many_n = w.too_many_n
+		elif isinstance(w, (ProcessedReadWriter, Demultiplexer)):
+			written = w.written
+			written_bp = w.written_bp
+
+	with_adapters = [0, 0]
+	for i in (0, 1):
+		for adapter in adapters_pair[i]:
+			with_adapters[i] += sum(adapter.lengths_front.values())
+			with_adapters[i] += sum(adapter.lengths_back.values())
+	quality_trimmed_bp = [ int(qtrimmed(modifiers) or 0),
+		int(qtrimmed(modifiers2) or 0) ]
+	total_bp = sum(stats.total_bp)
+	sep = "\t"
+	fields = ["OK", n, total_bp, too_short, too_long, too_many_n, written,
+		with_adapters[0], quality_trimmed_bp[0], written_bp[0]]
+	if paired:
+		fields.extend( [with_adapters[1], quality_trimmed_bp[1], written_bp[1]] )
+	warnbase = None
+	for which_in_pair in (0, 1):
+		for index, adapter in enumerate(adapters_pair[which_in_pair]):
+			total = sum(adapter.adjacent_bases.values())
+			for base in ['A', 'C', 'G', 'T', '']:
+				b = base if base != '' else 'none/other'
+				fraction = 1.0 * adapter.adjacent_bases[base] / total
+				if fraction > 0.8 and base != '':
+					warnbase = b
+			if total >= 20 and warnbase is not None:
+				fields[0] = "WARN"	
+
+	print( sep.join(map(str,fields)) )
+	sys.stdout = old_stdout
diff -rupN '--exclude=.git' cutadapt/cutadapt/scripts/cutadapt.py cutadapt_patched/cutadapt/scripts/cutadapt.py
--- cutadapt/cutadapt/scripts/cutadapt.py	2015-03-26 13:00:26.163894349 -0500
+++ cutadapt_patched/cutadapt/scripts/cutadapt.py	2015-03-26 12:16:52.509715125 -0500
@@ -79,7 +79,7 @@ from cutadapt.modifiers import (LengthTa
     NEndTrimmer)
 from cutadapt.writers import (TooShortReadFilter, TooLongReadFilter,
 	ProcessedReadWriter, Demultiplexer, NContentTrimmer)
-from cutadapt.report import Statistics, print_statistics
+from cutadapt.report import Statistics, print_statistics, print_succinct
 from cutadapt.compat import next
 
 logger = logging.getLogger(__name__)
@@ -425,6 +425,19 @@ def get_option_parser():
 	group = OptionGroup(parser, "Options that influence what gets output to where")
 	group.add_option("--quiet", default=False, action='store_true',
 		help="Do not print a report at the end.")
+	group.add_option("--succinct", default=False, action='store_true',
+		help="Print a single-line, tab-delimited summary. The fields are: "
+			"status, "
+			"reads/pairs processed, "
+			"total bp processed, "
+			"reads/pairs too short, "
+			"reads/pairs too long, "
+			"reads/pairs with too many N, "
+			"reads/pairs written, "
+			"AND for each individual read file: "
+			"reads w/ adapters, "
+			"bases quality-trimmed, "
+			"bases written.")
 	group.add_option("-o", "--output", metavar="FILE",
 		help="Write modified reads to FILE. FASTQ or FASTA format is chosen "
 			"depending on input. The summary report is sent to standard output. "
@@ -745,11 +758,12 @@ def main(cmdlineargs=None, default_outfi
 	if options.output:
 		logger.root.handlers = []
 		logging.basicConfig(level=logging.INFO, format='%(message)s', stream=sys.stdout)
-	logger.info("This is cutadapt %s with Python %s", __version__, platform.python_version())
-	logger.info("Command line parameters: %s", " ".join(cmdlineargs))
-	logger.info("Trimming %s adapter(s) with at most %.1f%% errors in %s mode ...",
-		len(adapters) + len(adapters2), options.error_rate * 100,
-		{ False: 'single-end', 'first': 'paired-end legacy', 'both': 'paired-end' }[paired])
+	if not options.succinct:
+		logger.info("This is cutadapt %s with Python %s", __version__, platform.python_version())
+		logger.info("Command line parameters: %s", " ".join(cmdlineargs))
+		logger.info("Trimming %s adapter(s) with at most %.1f%% errors in %s mode ...",
+			len(adapters) + len(adapters2), options.error_rate * 100,
+			{ False: 'single-end', 'first': 'paired-end legacy', 'both': 'paired-end' }[paired])
 
 	try:
 		reader = seqio.open(input_filename, file2=input_paired_filename,
@@ -851,7 +865,11 @@ def main(cmdlineargs=None, default_outfi
 			f.close()
 
 	elapsed_time = time.clock() - start_time
-	if not options.quiet:
+	if options.succinct:
+		stat_file = sys.stderr if options.output is None else None
+		print_succinct((adapters, adapters2), paired, stats,
+			modifiers, modifiers2, writers, file=stat_file)
+	elif not options.quiet:
 		# send statistics to stderr if result was sent to stdout
 		stat_file = sys.stderr if options.output is None else None
 		print_statistics((adapters, adapters2), paired, elapsed_time, stats,