sys.path.insert(1, current_script_dir)
import utils
import plotting
# ----------------------------------------------------------------------------------------
datadir = 'data/imgt'
xtitles = {
'indels' : 'fraction of positions indel\'d',
'subs' : 'substitution fraction'
}
glfo = utils.read_germline_set(datadir)
vgenes = glfo['aligned-genes']['v'].keys()
pversions = OrderedDict()
for vg in vgenes:
pv = utils.primary_version(vg)
if pv not in pversions:
pversions[pv] = []
pversions[pv].append(vg)
# remove primary versions that only have one gene
for pv in pversions:
if len(pversions[pv]) == 1:
print 'removing single-gene pv %s' % pv
del pversions[pv]
# ----------------------------------------------------------------------------------------
def indel_difference_fraction(seq1, seq2):
""" fraction of positions in the aligned sequences <seq1> <seq2> which are dots in exactly one of them """
if len(seq1) != len(seq2):
raise Exception('sequences different length:\n %s\n %s' % (seq1, seq2))
import utils
import glutils
import plotting
# ----------------------------------------------------------------------------------------
datadir = 'data/germlines/human'
xtitles = {
'indels' : 'fraction of positions indel\'d',
'subs' : 'substitution fraction'
}
glfo = glutils.read_glfo(datadir)
vgenes = glfo['aligned-genes']['v'].keys()
pversions = OrderedDict()
for vg in vgenes:
pv = utils.primary_version(vg)
if pv not in pversions:
pversions[pv] = []
pversions[pv].append(vg)
# remove primary versions that only have one gene
for pv in pversions:
if len(pversions[pv]) == 1:
print 'removing single-gene pv %s' % pv
del pversions[pv]
# ----------------------------------------------------------------------------------------
def indel_difference_fraction(seq1, seq2):
""" fraction of positions in the aligned sequences <seq1> <seq2> which are dots in exactly one of them """
if len(seq1) != len(seq2):
raise Exception('sequences different length:\n %s\n %s' % (seq1, seq2))
def get_base(gene):
basestr = utils.primary_version(gene)
if utils.sub_version(gene) is not None:
basestr += '-' + utils.sub_version(gene)
return basestr
sorted(set([get_base(g) for g in glfo['seqs'][args.region]])))))
args.other_genes = utils.get_arg_list(args.other_genes)
if args.other_genes is not None:
genes += args.other_genes
seqstrs = ['' for _ in range(len(genes))]
snpstrs = ['' for _ in range(len(genes))]
gene_str_width = max(
[utils.len_excluding_colors(utils.color_gene(g)) for g in genes])
codon_positions = glfo[utils.conserved_codons[args.locus][args.region] +
'-positions'] if args.region != 'd' else None
max_seq_len = max([len(glfo['seqs'][args.region][g]) for g in genes])
ref_gene = genes[0] if args.ref_allele is None else utils.rejoin_gene(
args.locus, args.region, utils.primary_version(genes[0]),
utils.sub_version(genes[0]), args.ref_allele)
if ref_gene != genes[0]:
genes.remove(ref_gene)
genes.insert(0, ref_gene)
ref_seq = glfo['seqs'][args.region][ref_gene]
ref_pos = codon_positions[ref_gene]
for igene in range(0, len(genes)):
gene = genes[igene]
seq = glfo['seqs'][args.region][gene]
pos = codon_positions[gene]
if pos < ref_pos: # align the codon position in the case that this seq is shorter up to the codon
seq = (ref_pos - pos) * '-' + seq
pos += (ref_pos - pos)
sys.path.insert(1, partis_dir + '/python')
import utils
import glutils
parser = argparse.ArgumentParser()
parser.add_argument('--base', required=True)
parser.add_argument('--alleles')
parser.add_argument('--other-genes')
parser.add_argument('--region', default='v')
parser.add_argument('--chain', default='h')
parser.add_argument('--glfo-dir', default='data/germlines/human')
args = parser.parse_args()
glfo = glutils.read_glfo(args.glfo_dir, args.chain)
if args.alleles is None:
args.alleles = [utils.allele(g) for g in glfo['seqs'][args.region] if args.base == utils.primary_version(g) + '-' + utils.sub_version(g)]
else:
args.alleles = utils.get_arg_list(args.alleles)
args.other_genes = utils.get_arg_list(args.other_genes)
# for g, s in glfo['seqs']['v'].items():
# print '%s %3d' % (utils.color_gene(g, width=20), len(s) - glfo['cyst-positions'][g])
# sys.exit()
# base = '4-59'
# a1, a2 = '12', '01'
# gene1, gene2 = 'IGHV' + base + '*' + a1, 'IGHV' + base + '*' + a2
genes = ['IG' + args.chain.upper() + args.region.upper() + args.base + '*' + al for al in args.alleles]
if args.other_genes is not None:
genes += args.other_genes
import utils
import glutils
parser = argparse.ArgumentParser()
parser.add_argument('--base', required=True)
parser.add_argument('--alleles')
parser.add_argument('--other-genes')
parser.add_argument('--region', default='v')
parser.add_argument('--locus', default='igh', choices=utils.loci.keys())
parser.add_argument('--glfo-dir', default='data/germlines/human')
args = parser.parse_args()
glfo = glutils.read_glfo(args.glfo_dir, args.locus)
if args.alleles is None:
args.alleles = [
utils.allele(g) for g in glfo['seqs'][args.region]
if args.base == utils.primary_version(g) +
('-' +
utils.sub_version(g) if utils.sub_version(g) is not None else '')
]
else:
args.alleles = utils.get_arg_list(args.alleles)
if len(args.alleles) == 0:
raise Exception(
'couldn\'t find any alleles for --base %s. Other choices:\n %s' %
(args.base, ' '.join(glfo['seqs'][args.region])))
args.other_genes = utils.get_arg_list(args.other_genes)
# for g, s in glfo['seqs']['v'].items():
# print '%s %3d' % (utils.color_gene(g, width=20), len(s) - glfo['cyst-positions'][g])
# sys.exit()