def ids2cds(ql):
cdmic = CDMI_API(URLS.cdmi)
idm = IdMap(URLS.idmap)
gl = set()
rd = {}
eids = []
lids = set()
mids = set()
for gid in ql:
rd[gid] = gid
if 'kb|g.' in gid:
if 'locus' in gid:
lids.add(gid)
elif 'mRNA' in gid:
mids.add(gid)
else:
eids.append(gid)
sid2fids = cdmic.source_ids_to_fids(eids)
for sid in sid2fids:
for fid in sid2fids[sid]:
rd[sid] = fid
if 'locus' in fid:
lids.add(fid)
elif 'mRNA' in fid:
mids.add(fid)
lidmap = ()
if len(lids) > 0: lidmap = idm.longest_cds_from_locus(list(lids))
for lid in lidmap:
for k in lidmap[lid]:
gl.add(k)
midl = list(mids)
midmap = ()
if len(mids) > 0: lidmap = idm.longest_cds_from_mrna(list(mids))
for lid in midmap:
for k in midmap[lid]:
gl.add(k)
for gid in ql:
if 'kb|g.' in gid:
if 'locus' in gid:
for k in lidmap[gid]:
rd[gid] = k
elif 'mRNA' in gid:
for k in midmap[gid]:
rd[gid] = k
else:
if 'locus' in rd[gid]:
for k in lidmap[rd[gid]]:
rd[gid] = k
elif 'mRNA' in rd[gid]:
for k in midmap[rd[gid]]:
rd[gid] = k
return rd
def ids2cds(ql):
cdmic = CDMI_API(URLS.cdmi)
idm = IdMap(URLS.idmap)
gl = set()
rd = {}
eids = []
lids = set()
mids = set()
for gid in ql:
rd[gid] = gid
if 'kb|g.' in gid:
if 'locus' in gid:
lids.add(gid)
elif 'mRNA' in gid:
mids.add(gid)
else:
eids.append(gid)
sid2fids = cdmic.source_ids_to_fids(eids)
for sid in sid2fids:
for fid in sid2fids[sid]:
rd[sid] = fid
if 'locus' in fid:
lids.add(fid)
elif 'mRNA' in fid:
mids.add(fid)
lidmap = ()
if len(lids) > 0: lidmap = idm.longest_cds_from_locus(list(lids))
for lid in lidmap:
for k in lidmap[lid]:
gl.add(k)
midl = list(mids)
midmap = ()
if len(mids) > 0: lidmap = idm.longest_cds_from_mrna(list(mids))
for lid in midmap:
for k in midmap[lid]:
gl.add(k)
for gid in ql:
if 'kb|g.' in gid:
if 'locus' in gid:
for k in lidmap[gid]:
rd[gid] = k
elif 'mRNA' in gid:
for k in midmap[gid]:
rd[gid] = k
else:
if 'locus' in rd[gid]:
for k in lidmap[rd[gid]]:
rd[gid] = k
elif 'mRNA' in rd[gid]:
for k in midmap[rd[gid]]:
rd[gid] = k
return rd
