本文整理汇总了Python中khmer.ReadParser.close方法的典型用法代码示例。如果您正苦于以下问题：Python ReadParser.close方法的具体用法？Python ReadParser.close怎么用？Python ReadParser.close使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类khmer.ReadParser的用法示例。
在下文中一共展示了ReadParser.close方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: main
# 需要导入模块: from khmer import ReadParser [as 别名]
# 或者: from khmer.ReadParser import close [as 别名]
#.........这里部分代码省略.........
if args.output is None:
# note: this will be saved in trimfp.
outfp = open(os.path.basename(filename) + '.abundtrim', 'wb')
# get file handle w/gzip, bzip
trimfp = get_file_writer(outfp, args.gzip, args.bzip)
# record all this info
pass2list.append((filename, pass2filename, trimfp))
# input file stuff: get a broken_paired reader.
paired_iter = broken_paired_reader(ReadParser(filename), min_length=K,
force_single=args.ignore_pairs)
# main loop through the file.
n_start = trimmer.n_reads
save_start = trimmer.n_saved
watermark = REPORT_EVERY_N_READS
for read in trimmer.pass1(paired_iter, pass2fp):
if (trimmer.n_reads - n_start) > watermark:
log_info("... {filename} {n_saved} {n_reads} {n_bp} "
"{w_reads} {w_bp}", filename=filename,
n_saved=trimmer.n_saved, n_reads=trimmer.n_reads,
n_bp=trimmer.n_bp, w_reads=written_reads,
w_bp=written_bp)
watermark += REPORT_EVERY_N_READS
# write out the trimmed/etc sequences that AREN'T going to be
# revisited in a 2nd pass.
write_record(read, trimfp)
written_bp += len(read)
written_reads += 1
pass2fp.close()
log_info("{filename}: kept aside {kept} of {total} from first pass",
filename=filename, kept=trimmer.n_saved - save_start,
total=trimmer.n_reads - n_start)
# first pass goes across all the data, so record relevant stats...
n_reads = trimmer.n_reads
n_bp = trimmer.n_bp
n_skipped = trimmer.n_skipped
bp_skipped = trimmer.bp_skipped
save_pass2_total = trimmer.n_saved
# ### SECOND PASS. ###
# nothing should have been skipped yet!
assert trimmer.n_skipped == 0
assert trimmer.bp_skipped == 0
if args.single_pass:
pass2list = []
# go back through all the files again.
for _, pass2filename, trimfp in pass2list:
log_info('second pass: looking at sequences kept aside in {pass2}',
pass2=pass2filename)
# note that for this second pass, we don't care about paired
# reads - they will be output in the same order they're read in,
# so pairs will stay together if not orphaned. This is in contrast
# to the first loop. Hence, force_single=True below.
read_parser = ReadParser(pass2filename)示例2: reads
# 需要导入模块: from khmer import ReadParser [as 别名]
# 或者: from khmer.ReadParser import close [as 别名]
def reads():
infile = utils.get_test_data('valid-read-testing.fq')
reads = ReadParser(infile)
yield reads
reads.close()