from jcvi.formats.bed import Bed from jcvi.formats.sizes import Sizes from jcvi.formats.blast import Blast from jcvi.graphics.base import normalize_axes, plt, savefig from jcvi.graphics.dotplot import dotplot from jcvi.utils.cbook import gene_name, human_size from jcvi.utils.natsort import natsorted # Map orientations to ints FF = {'+': 1, '-': -1, '?': 1} RR = {'+': -1, '-': 1, '?': -1} LB = 18 # Lower bound for golden_array() UB = 29 # Upper bound for golden_array() BB = UB - LB + 1 # Span for golden_array() ACCEPT = green("ACCEPT") REJECT = red("REJECT") BINSIZE = 50000 class ContigOrderingLine(object): '''Stores one line in the ContigOrdering file ''' def __init__(self, line, sep="|"): args = line.split() self.contig_id = args[0] self.contig_name = args[1].split(sep)[0] contig_rc = args[2] assert contig_rc in ('0', '1') self.strand = '+' if contig_rc == '0' else '-' self.orientation_score = args[3] self.gap_size_after_contig = args[4]
from jcvi.formats.sizes import Sizes from jcvi.formats.blast import Blast from jcvi.graphics.base import normalize_axes, plt, savefig from jcvi.graphics.dotplot import dotplot from jcvi.utils.cbook import gene_name, human_size from jcvi.utils.natsort import natsorted # Map orientations to ints FF = {'+': 1, '-': -1, '?': 1} RR = {'+': -1, '-': 1, '?': -1} LB = 18 # Lower bound for golden_array() UB = 29 # Upper bound for golden_array() BB = UB - LB + 1 # Span for golden_array() ACCEPT = green("ACCEPT") REJECT = red("REJECT") BINSIZE = 50000 class ContigOrderingLine(object): '''Stores one line in the ContigOrdering file ''' def __init__(self, line, sep="|"): args = line.split() self.contig_id = args[0] self.contig_name = args[1].split(sep)[0] contig_rc = args[2] assert contig_rc in ('0', '1') self.strand = '+' if contig_rc == '0' else '-' self.orientation_score = args[3] self.gap_size_after_contig = args[4]