In [ ]:

    

config['out_extensions'] = ['eps', 'png', 'pdf']

MAX_ROWS        = 10000

NROWS           = 1000
NROWS           = 10000
NROWS           = None

PARSE_VERBOSE   = False
#PARSE_VERBOSE   = True

REPORT_SIZE     = True

HISTOGRAM_COLOR = (0.5,0.5,0.5)
ALL_GRAPH_COLOR = (0.2,0.2,0.2)

CHROM_FIG_SCALE_FACTOR_H = 2
CHROM_FIG_SCALE_FACTOR_W = 2

FULL_FIG_W , FULL_FIG_H  = (19 if REPORT_SIZE else 16) , 8
CHROM_FIG_W, CHROM_FIG_H = FULL_FIG_W/CHROM_FIG_SCALE_FACTOR_W, (FULL_FIG_W*2)/CHROM_FIG_SCALE_FACTOR_H


    

In [1]:

    

cols_to_plot = [
        # Col name                                 limit     # ticks color
        [ "K-mer Coverage"                       , [0,1]   , 5,      'red'       ], 
        [ "Sequencing Coverage"                  , None    , 5,      'green'     ],
        [ "Ns"                                   , [0.1,1] , 0,      'grey'      ],
        [ "AGP Contig"                           , [0.1,1] , 0,      'grey'      ],
        [ "AGP Gap"                              , [0.1,1] , 0,      'grey'      ],
        None, #[ "AGP Unknown"                          , [0.1,1] , 0,      'grey'      ],
        None, #[ "AGP Other"                            , [0.1,1] , 0,      'grey'      ],
        [ "K-mer Coverage averaged: 500 bp"      , [0,None], 1,      'indianred' ],
        None, #[ "K-mer Coverage averaged: 2.5 Kbp"     , [0,None], 2,      'limegreen' ],
        [ "K-mer Coverage averaged: 5 Kbp"       , [0,None], 1,      'cyan'      ],
        None, #[ "K-mer Coverage averaged: 50 Kbp"      , [0,None], 2,      'orange'    ],
        [ "K-mer Coverage averaged: 1 Mbp"       , [0,None], 1,      'olive'     ],
        None, #[ "K-mer Coverage averaged: 5 Kbp before", [0,None], 2,      'violet'    ],
        None #[ "K-mer Coverage averaged: 5 Kbp after" , [0,None], 2,      'maroon'    ]
    ]

BAC_MODE     = False
if 'BAC' in config:
    BAC_MODE = True
    cols_to_plot.insert(2, ['BLAST Coverage', [0, None], 5, 'blue' ])
else:
    cols_to_plot.insert(2, None)


    

    




---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-1-5e7adbf14d9b> in <module>()
     18 
     19 BAC_MODE     = False
---> 20 if 'BAC' in config:
     21     BAC_MODE = True
     22     cols_to_plot.insert(2, ['BLAST Coverage', [0, None], 5, 'blue' ])

NameError: name 'config' is not defined