def parse_dups(dups_file, flat):
#####THIS ONLY WORKS IF WE CHANGE QUOTA
flat.fill_dict()
dup_dic = {}
seen = []
for line in open(dups_file):
line = line.strip().split("\t")
parent = line[0]
dups = line[1:]
all = [Bed.row_to_dict(flat.d[f]) for f in list(set(line))]
all.sort(key=operator.itemgetter('start'))
dup_start = all[0]
dup_end = all[-1]
dup_dic[parent] = 'P'
seen += [parent]
for dup in dups:
if dup in seen: continue
seen.append(dup)
dup_dic[dup] = parent
# so here, there are all the genes that arent part of the local dup
# array, but we want to mark them with 'I'
intervening = flat.get_features_in_region(dup_start['seqid'], dup_start['start'], dup_end['end'])
for ii in intervening:
if ii['accn'] == parent or ii['accn'] == dup_end: continue
if not ii['accn'] in dup_dic.keys():
dup_dic[ii['accn']] = 'I'
return dup_dic
def write_genelist(q_or_s, outfile, flat, pairs, orthos, mcnss, link_fmt, this_org, other_org,
other_flat, dups, local_dups):
# used in the link_fmt
qorg, sorg = this_org, other_org
fmt = "%(accn)s\t%(seqid)s\t%(start)i\t%(end)i\t%(ortholog)s\t%(ortho_cns)s\t"
fmt +="%(regional_dup_info)s\t%(local_dup_info)s\t%(strand)s\t"
fmt += "%(new_gene_info)s\t%(link)s"
header = fmt.replace('%(', '').replace(')s','').replace(')i','')
outdir = op.dirname(flat.path)
annos = dict([kv.rstrip().split(",") for kv in open("%s/%s_protein_rna.anno" % (outdir, q_or_s))])
if flat.path == other_flat.path:
annos.update(dict([kv.rstrip().split(",") for kv in open("%s/s_protein_rna.anno" % (outdir,))]))
out = open(outfile, 'w')
print >>sys.stderr, "writing genelist to %s" % (outfile,)
print >>out, header.replace('ortho_', other_org + '_')
same_org = this_org == other_org
for feat in flat:
these_pairs = pairs.get(feat['accn'], [])
cnss = mcnss.get(feat['accn'], [])
ortholog, other_pairs = split_pairs(feat, [other_flat.d[t] for t in these_pairs], orthos, q_or_s=='s')
ortho_cns, non_ortho_cns = split_cns(cnss, orthos, q_or_s=='s')
regional_dup_info = dups.get(feat['accn'], '')
local_dup_info = local_dups.get(feat['accn'], '')
if ortholog:
ortho = ortholog[0]
link = link_fmt % dict(qorg=qorg, sorg=sorg,
accn1=ortho['accn'], accn2=feat['accn']
)
else:
link = ''
new_gene_info = ""
if feat['accn'].endswith(("_cns_protein", "_cns_rna")):
try:
new_gene_info = annos[feat['accn']]
except KeyError: # from coannoation of previous run.
pass
ortholog = len(ortholog) and ",".join([o["accn"] for o in ortholog]) or ""
if len(ortho_cns) > 0 and len(ortholog) == 0:
print >>sys.stderr, "\nBAD", feat, "\n", ortho_cns, "\nthese:", these_pairs, "\nother:", other_pairs, "\n\n"
# fell right on the edge of a syntenic block. the cns got in, but not the gene.
#1/0
other_pairs = ",".join([o["accn"] for o in other_pairs])
fmt_dict = locals()
fmt_dict.update(Bed.row_to_dict(feat))
fmt_dict.update({'ortho_cns': len(ortho_cns) if ortholog else "",
'ortho_NON_cns_count': len(non_ortho_cns) if
other_pairs else ""})
print >>out, fmt % fmt_dict
