"have this increment: ex: #>10000 "
"Default: 10000 ")
],
[
"counts", "counts", argflag, False,
("Graph counts instead of bases ie. number of reads")
],
[
"out", "out", str, "cellstats.pdf",
("Output filename. Default: 'cellstats.pdf'")
]]
arguments = map(CLArgument._make, argument_list)
if not len(sys.argv) > 1:
sys.exit(getHelpStr(description, arguments) + "\n")
(p_arg_map, args_remaining) = parseArgs(sys.argv[1:], arguments)
if not len(args_remaining) >= 1:
sys.exit(getHelpStr(description, arguments) + "\n")
title = args_remaining[0]
infiles = args_remaining[1:]
cellnames = map(lambda f: "_".join(f.split(".")[0].split("_")[:2]), infiles)
fit_gen = lambda filename: fileIterator(filename, lineItemIterator)
file_iterators = map(fit_gen, infiles)
from seqio import iteratorFromExtension, seqlen, recordToString
from nucio import fileIterator
from args import parseArgs, getHelpStr, CLArgument
description = (
"Usage: length_filter.py [options] min_length(int) in1.{fa.fq} [in2.{fa,fq} ...]\n\n"
"Filter reads by their lengths"
)
argument_list = [["maxlen", "maxlen", int, -1, "Maximum length of reads"]]
arguments = map(CLArgument._make, argument_list)
if not len(sys.argv) > 2:
sys.exit(getHelpStr(description, arguments) + "\n")
(p_arg_map, args_remaining) = parseArgs(sys.argv[1:], arguments)
minlen = int(args_remaining[0])
files = args_remaining[1:]
if not all(map(os.path.exists, files)):
sys.exit("Not all files exist")
file_readers = starmap(fileIterator, zip(files, map(iteratorFromExtension, files)))
filt_cond = lambda record: seqlen(record) > minlen
if p_arg_map["maxlen"] > 1:
description = ("lengthhist.py [options] title alginments.m4 [alignments2.m4...]\n"
"Plot Make histograms from alignment (nucmer show-coords) "
"files")
argument_list = [["labels","labels",arglist,["Ectools","PacbioToCA"], "Labels for each dataset"],
["ymax", "ymax", int, -1, "Maximum Y-value"],
["lenfiles", "lenfiles", int, -1, ("Input files are just a column of lengths, "
"argument specifies the column")]]
args = map(CLArgument._make, argument_list)
(parg_map, args_remaining) = parseArgs(sys.argv[1:],args)
if not len(args_remaining) >= 3:
sys.exit(getHelpStr(description,args) + "\n")
title = args_remaining[0]
igetter = attrgetter("qseqlength")
flens = []
for fname in args_remaining[1:]:
with open(fname) as fh:
if parg_map["lenfiles"] < 0:
records = lineRecordIterator(fh, M4Record, M4RecordTypes)
flens.append( map(igetter, records) )
else:
getter = itemgetter(parg_map["lenfiles"])
flens.append( map(int, imap(getter, lineItemIterator(fh) )))
pp = PdfPages("hist.pdf")
