def read_glfo(gldir, chain, only_genes=None, skip_pseudogenes=True, debug=False):
if not os.path.exists(gldir + "/" + chain):
raise Exception(
"germline set directory '%s' does not exist (maybe --parameter-dir is corrupted, maybe crashed while writing parameters?)"
% (gldir + "/" + chain)
)
if debug:
print " reading %s chain glfo from %s" % (chain, gldir)
glfo = {"chain": chain}
glfo["seqs"] = read_germline_seqs(gldir, chain, skip_pseudogenes)
read_extra_info(glfo, gldir)
get_missing_codon_info(glfo, debug=debug)
restrict_to_genes(glfo, only_genes, debug=debug)
for region, codon in utils.conserved_codons[glfo["chain"]].items():
seqons = [
(seq, glfo[codon + "-positions"][gene]) for gene, seq in glfo["seqs"][region].items()
] # (seq, pos) pairs
utils.check_a_bunch_of_codons(codon, seqons, extra_str=" ", debug=debug)
if debug:
print " read %s" % " ".join([("%s: %d" % (r, len(glfo["seqs"][r]))) for r in utils.regions])
return glfo
def get_missing_codon_info(glfo, debug=False):
# ----------------------------------------------------------------------------------------
def get_n_gaps_up_to_pos(aligned_seq, pos):
# NOTE I think this duplicates the functionality of count_gaps()
""" return number of gapped positions in <aligned_seq> before <pos> """
ipos = 0 # position in unaligned sequence
n_gaps_passed = (
0
) # number of gapped positions in the aligned sequence that we pass before getting to <pos> (i.e. while ipos < pos)
while ipos < pos:
if aligned_seq[ipos + n_gaps_passed] in utils.gap_chars:
n_gaps_passed += 1
else:
ipos += 1
return n_gaps_passed
# ----------------------------------------------------------------------------------------
def get_pos_in_alignment(codon, aligned_seq, seq, pos):
""" given <pos> in <seq>, find the codon's position in <aligned_seq> """
assert utils.codon_ok(
codon, seq, pos, debug=debug
) # this only gets called on the gene with the *known* position, so it shouldn't fail
pos_in_alignment = pos + get_n_gaps_up_to_pos(aligned_seq, pos)
assert utils.codon_ok(codon, aligned_seq, pos_in_alignment, debug=debug)
return pos_in_alignment
for region, codon in utils.conserved_codons[glfo["chain"]].items():
missing_genes = set(glfo["seqs"][region]) - set(glfo[codon + "-positions"])
if len(missing_genes) == 0:
if debug:
print " no missing %s info" % codon
continue
if debug:
print " missing %d %s positions" % (len(missing_genes), codon)
aligned_seqs = get_new_alignments(glfo, region, debug=debug)
# for g, s in aligned_seqs.items():
# print s, utils.color_gene(g)
# if region == 'j':
# raise Exception('missing tryp position for %s, and we can\'t infer it because tryp positions don\'t reliably align to the same position' % ' '.join(missing_genes))
# existing codon position (this assumes that once aligned, all genes have the same codon position -- which is only really true for the imgt-gapped alignment)
if len(glfo[codon + "-positions"]) > 0:
known_gene, known_pos = None, None
for gene, pos in glfo[
codon + "-positions"
].items(): # take the first one for which we have the sequence (NOTE it would be safer to check that they're all the same)
if (
gene in glfo["seqs"][region]
and gene in aligned_seqs
and utils.codon_ok(codon, glfo["seqs"][region][gene], pos)
):
known_gene, known_pos = gene, pos
break
if known_gene is None:
raise Exception("couldn't find a known %s position" % codon)
# NOTE for cyst, should be 309 if alignments are imgt [which they used to usually be, but now probably aren't] (imgt says 104th codon --> subtract 1 to get zero-indexing, then multiply by three 3 * (104 - 1) = 309
known_pos_in_alignment = get_pos_in_alignment(
codon, aligned_seqs[known_gene], glfo["seqs"][region][known_gene], known_pos
)
if debug:
print " using known position %d (aligned %d) in %s" % (
known_pos,
known_pos_in_alignment,
known_gene,
)
elif codon == "cyst":
known_pos_in_alignment = 309
print " assuming aligned %s position is %d (this will %s work if you're using imgt alignments)" % (
codon,
known_pos_in_alignment,
utils.color("red", "only"),
)
raise Exception("not really using imgt alignments much any more, so this isn't really going to work")
else:
raise Exception("no existing %s info, and couldn't guess it, either" % codon)
n_added = 0
seqons = [] # (seq, pos) pairs
for gene in missing_genes:
unaligned_pos = known_pos_in_alignment - utils.count_gaps(aligned_seqs[gene], istop=known_pos_in_alignment)
seq_to_check = glfo["seqs"][region][gene]
seqons.append((seq_to_check, unaligned_pos))
glfo[codon + "-positions"][gene] = unaligned_pos
n_added += 1
# if debug:
# tmpseq = aligned_seqs[gene]
# tmppos = known_pos_in_alignment
# print ' %s%s%s %s (new)' % (tmpseq[:tmppos], utils.color('reverse_video', tmpseq[tmppos : tmppos + 3]), tmpseq[tmppos + 3:], utils.color_gene(gene))
utils.check_a_bunch_of_codons(codon, seqons, extra_str=" ", debug=debug)
if debug:
print " added %d %s positions" % (n_added, codon)
