# Path: nucio.py
# def lineRecordIterator(fh, nt, nt_types, filter_func=trueFunc, delim=None, cleaner_func=None):
# def lineItemIterator(fh, filter_func=trueFunc):
# def getNucmerAlignmentIterator(fh):
# def fileIterator(filename, itemIterator, open_func=open):
# def recordToString( record, delim="\t" ):
# def nucRecordToString(nuc_record):
# def typeify(mylist, mytypes):
# def prepareDeltaRecord(buf):
# def getDeltaAlignmentIterator(fh):
# def deltaRecordHeaderToString(dr):
# def deltaAlignmentHeaderToString(alignment):
# def deltaRecordToOriginalFormat(dr):
#     def __init__(self, s, *args ):
#     def __enter__(self):
#     def __exit__(self, ttype ,value, traceback):
# def openerFromExtension(filename, default=None):
# class FileOrStream:


import sys
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
from operator import attrgetter, itemgetter
from itertools import imap
from matplotlib.backends.backend_pdf import PdfPages
from nucio import lineRecordIterator, M4Record, M4RecordTypes, lineItemIterator
from args import arglist, parseArgs, getHelpStr, CLArgument, argflag
#!/usr/bin/env python


mpl.use('Agg')



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")


# Path: nucio.py
# def lineRecordIterator(fh, nt, nt_types, filter_func=trueFunc, delim=None, cleaner_func=None):
# def lineItemIterator(fh, filter_func=trueFunc):
# def getNucmerAlignmentIterator(fh):
# def fileIterator(filename, itemIterator, open_func=open):
# def recordToString( record, delim="\t" ):
# def nucRecordToString(nuc_record):
# def typeify(mylist, mytypes):
# def prepareDeltaRecord(buf):
# def getDeltaAlignmentIterator(fh):
# def deltaRecordHeaderToString(dr):
# def deltaAlignmentHeaderToString(alignment):
# def deltaRecordToOriginalFormat(dr):
#     def __init__(self, s, *args ):
#     def __enter__(self):
#     def __exit__(self, ttype ,value, traceback):
# def openerFromExtension(filename, default=None):
# class FileOrStream:


# Path: lengthhist.py
import sys
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
from operator import attrgetter, itemgetter
from itertools import imap
from matplotlib.backends.backend_pdf import PdfPages
from nucio import lineRecordIterator, M4Record, M4RecordTypes, lineItemIterator
from args import arglist, parseArgs, getHelpStr, CLArgument, argflag

#!/usr/bin/env python


mpl.use('Agg')



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 = []