cutadapt "succinct" patch (original) (raw)

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,