def test_intersect(self):
# Test from the snp workflow.
expected = ('chr',91143,91144, ('C','*A','0','|EBMYCG00000002479|Rv0083',1,0))
a = genrep.Assembly('mycoTube_H37RV')
c = concat_fields(a.annot_track('CDS','chr'), infields=['name','strand','frame'], as_tuple=True)
feat = fstream([('chr',91143,91144,('C','*A','0'))], fields=['chr','start','end','rest'])
g = intersect([feat,c], win_size=10000)
self.assertEqual(g.next(),expected)
fields = ['chr','start','end','name','strand','score']
s1 = fstream([('chr',0,20,'a1',1,6.),('chr',40,60,'b',1,3.)], fields=fields)
s2 = fstream([('chr',10,30,'a2',1,8.),('chr',50,70,'b',-1,4.)], fields=fields)
res = list(intersect([s1,s2]))
expected = [('chr',10,20,'a1|a2',1,14.),('chr',50,60,'b|b',0,7.)]
self.assertListEqual(res,expected)
def test_intersect(self):
# Test from the snp workflow.
expected = ('chr', 91143, 91144, ('C', '*A', '0',
'|EBMYCG00000002479|Rv0083', 1, 0))
a = genrep.Assembly('mycoTube_H37RV')
c = concat_fields(a.annot_track('CDS', 'chr'),
infields=['name', 'strand', 'frame'],
as_tuple=True)
feat = fstream([('chr', 91143, 91144, ('C', '*A', '0'))],
fields=['chr', 'start', 'end', 'rest'])
g = intersect([feat, c], win_size=10000)
self.assertEqual(g.next(), expected)
fields = ['chr', 'start', 'end', 'name', 'strand', 'score']
s1 = fstream([('chr', 0, 20, 'a1', 1, 6.),
('chr', 40, 60, 'b', 1, 3.)],
fields=fields)
s2 = fstream([('chr', 10, 30, 'a2', 1, 8.),
('chr', 50, 70, 'b', -1, 4.)],
fields=fields)
res = list(intersect([s1, s2]))
expected = [('chr', 10, 20, 'a1|a2', 1, 14.),
('chr', 50, 60, 'b|b', 0, 7.)]
self.assertListEqual(res, expected)
def exon_snps(chrom,outexons,allsnps,assembly,sample_names,genomeRef={},
logfile=sys.stdout,debugfile=sys.stderr):
"""Annotates SNPs described in `filedict` (a dictionary of the form {chromosome: filename}
where `filename` is an output of parse_pileupFile).
Adds columns 'gene', 'location_type' and 'distance' to the output of parse_pileupFile.
Returns two files: the first contains all SNPs annotated with their position respective to genes in
the specified assembly, and the second contains only SNPs found within CDS regions.
:param chrom: (str) chromosome name.
:param outexons: (str) name of the file containing the list of SNPs on exons.
:param allsnps: list of tuples (chr,start,end,ref,alt1..altN) as returned by all_snps().
Ex: [('chr', 3684115, 3684116, 'G', 'G', 'G', 'G', 'T (56% of 167)', 'G'), ...]
:param assembly: genrep.Assembly object
:param sample_names: list of sample names.
:param genomeRef: dict of the form {'chr1': filename}, where filename is the name of a fasta file
containing the reference sequence for the chromosome.
"""
def _write_buffer(_buffer, outex):
new_codon = None
# One position at a time
for chr,pos,refbase,variants,cds,strand,ref_codon,shift in _buffer:
varbase = list(variants) # Ex: ['G','G','G','T (56% of 167)','G'], ['A/A','G/G (100% of 7)']
if new_codon is None:
new_codon = [[ref_codon] for _ in range(len(varbase))]
variants = [] # [[variants sample1], [variants sample2], ...]
# One sample at a time
for variant in varbase:
if variant in ['0','-']:
variants.append([refbase])
else: # Ex: 'C/G (80% of 10)' : heterozygous simple (ref is C) or double snp (ref is not C)
v = variant.split()[0] # Ex: C/G
v = unique(v.split('/')) # Ex: G/G -> 'G'
if refbase in v: v.remove(refbase) # Ex: C/G -> 'G' (if ref is C)
variants.append(v)
# One sample at a time
for k,v in enumerate(variants):
cnumb = len(new_codon[k])
newc = new_codon[k]*len(v)
for i,vari in enumerate(v):
for j in range(cnumb):
newc[i*cnumb+j] = newc[i*cnumb+j][:shift] +vari +newc[i*cnumb+j][shift+1:]
assert ref_codon[shift] == refbase, "bug with shift within codon"
new_codon[k] = newc
if new_codon is None: return
if strand == -1:
ref_codon = revcomp(ref_codon)
new_codon = [[revcomp(s) for s in c] for c in new_codon]
for chr,pos,refbase,variants,cds,strand,dummy,shift in _buffer:
refc = [iupac.get(x,x) for x in ref_codon]
ref_codon = [''.join(x) for x in product(*refc)]
newc = [[[iupac.get(x,x) for x in variant] for variant in sample]
for sample in new_codon]
new_codon = [[''.join(x) for codon in sample for x in product(*codon)] for sample in newc]
if refbase == "*":
result = [chr, pos+1, refbase] + list(variants) + [cds, strand] \
+ [','.join([translate.get(refc,'?') for refc in ref_codon])] + ["indel"]
else:
result = [chr, pos+1, refbase] + list(variants) + [cds, strand] \
+ [','.join([translate.get(refc,'?') for refc in ref_codon])] \
+ [','.join([translate.get(s,'?') for s in newc]) for newc in new_codon]
outex.write("\t".join([str(r) for r in result])+"\n")
#############################################################
snp_stream = FeatureStream(allsnps, fields=['chr','start','end','ref']+sample_names)
inclstream = concat_fields(snp_stream, infields=snp_stream.fields[3:], as_tuple=True)
snp_stream = FeatureStream(allsnps, fields=['chr','start','end','ref']+sample_names)
inclstream = concat_fields(snp_stream, infields=snp_stream.fields[3:], as_tuple=True)
try:
annotstream = concat_fields(assembly.annot_track('CDS',chrom),
infields=['name','strand','frame'], as_tuple=True)
annotstream = FeatureStream((x[:3]+(x[1:3]+x[3],) for x in annotstream),fields=annotstream.fields)
except:
return False
_buffer = {1:[], -1:[]}
last_start = {1:-1, -1:-1}
logfile.write(" Intersection with CDS - codon changes\n"); logfile.flush()
outex = open(outexons,"a")
for x in gm_stream.intersect([inclstream, annotstream]):
# x = (chr, start,end, (alt1,alt2, , start1,end1,cds1,strand1,phase1, start2,end2,cds2,strand2,phase2 ))
# x = ('chrV',1606,1607, ('T','C (43%)', 1612,1724,'YEL077C|YEL077C',-1,0, 1712,1723,'YEL077W-A|YEL077W-A',1,0))
nsamples = len(sample_names)
chr = x[0]; pos = x[1]; rest = x[3]
refbase = rest[0]
annot = [rest[5*i+nsamples+1 : 5*i+5+nsamples+1]
for i in range(len(rest[nsamples+1:])/5)] # list of (start,end,cds,strand,phase)
for es,ee,cds,strand,phase in annot:
if strand == 1:
shift = (pos-es-phase) % 3
elif strand == -1:
shift = (pos-ee+phase) % 3
else:
continue
codon_start = pos-shift
ref_codon = assembly.fasta_from_regions({chr: [[codon_start,codon_start+3]]}, out={},
path_to_ref=genomeRef.get(chr))[0][chr][0]
info = [chr,pos,refbase,list(rest[1:nsamples+1]),cds,strand,
ref_codon.upper(),shift]
# Either the codon is the same as the previous one on this strand, or it will never be.
# Only if one codon is passed, can write its snps to a file.
if codon_start == last_start[strand]:
_buffer[strand].append(info)
else:
_write_buffer(_buffer[strand],outex)
_buffer[strand] = [info]
last_start[strand] = codon_start
for strand in [1,-1]:
_write_buffer(_buffer[strand],outex)
outex.close()
return True
def exon_snps(chrom,
outexons,
allsnps,
assembly,
sample_names,
genomeRef={},
logfile=sys.stdout,
debugfile=sys.stderr):
"""Annotates SNPs described in `filedict` (a dictionary of the form {chromosome: filename}
where `filename` is an output of parse_pileupFile).
Adds columns 'gene', 'location_type' and 'distance' to the output of parse_pileupFile.
Returns two files: the first contains all SNPs annotated with their position respective to genes in
the specified assembly, and the second contains only SNPs found within CDS regions.
:param chrom: (str) chromosome name.
:param outexons: (str) name of the file containing the list of SNPs on exons.
:param allsnps: list of tuples (chr,start,end,ref,alt1..altN) as returned by all_snps().
Ex: [('chr', 3684115, 3684116, 'G', 'G', 'G', 'G', 'T (56% of 167)', 'G'), ...]
:param assembly: genrep.Assembly object
:param sample_names: list of sample names.
:param genomeRef: dict of the form {'chr1': filename}, where filename is the name of a fasta file
containing the reference sequence for the chromosome.
"""
def _write_buffer(_buffer, outex):
new_codon = None
# One position at a time
for chr, pos, refbase, variants, cds, strand, ref_codon, shift in _buffer:
varbase = list(
variants
) # Ex: ['G','G','G','T (56% of 167)','G'], ['A/A','G/G (100% of 7)']
if new_codon is None:
new_codon = [[ref_codon] for _ in range(len(varbase))]
variants = [] # [[variants sample1], [variants sample2], ...]
# One sample at a time
for variant in varbase:
if variant in ['0', '-']:
variants.append([refbase])
else: # Ex: 'C/G (80% of 10)' : heterozygous simple (ref is C) or double snp (ref is not C)
v = variant.split()[0] # Ex: C/G
v = unique(v.split('/')) # Ex: G/G -> 'G'
if refbase in v:
v.remove(refbase) # Ex: C/G -> 'G' (if ref is C)
variants.append(v)
# One sample at a time
for k, v in enumerate(variants):
cnumb = len(new_codon[k])
newc = new_codon[k] * len(v)
for i, vari in enumerate(v):
for j in range(cnumb):
newc[i * cnumb +
j] = newc[i * cnumb +
j][:shift] + vari + newc[i * cnumb +
j][shift + 1:]
assert ref_codon[
shift] == refbase, "bug with shift within codon"
new_codon[k] = newc
if new_codon is None: return
if strand == -1:
ref_codon = revcomp(ref_codon)
new_codon = [[revcomp(s) for s in c] for c in new_codon]
for chr, pos, refbase, variants, cds, strand, dummy, shift in _buffer:
refc = [iupac.get(x, x) for x in ref_codon]
ref_codon = [''.join(x) for x in product(*refc)]
newc = [[[iupac.get(x, x) for x in variant] for variant in sample]
for sample in new_codon]
new_codon = [[
''.join(x) for codon in sample for x in product(*codon)
] for sample in newc]
if refbase == "*":
result = [chr, pos+1, refbase] + list(variants) + [cds, strand] \
+ [','.join([translate.get(refc,'?') for refc in ref_codon])] + ["indel"]
else:
result = [chr, pos+1, refbase] + list(variants) + [cds, strand] \
+ [','.join([translate.get(refc,'?') for refc in ref_codon])] \
+ [','.join([translate.get(s,'?') for s in newc]) for newc in new_codon]
outex.write("\t".join([str(r) for r in result]) + "\n")
#############################################################
snp_stream = FeatureStream(allsnps,
fields=['chr', 'start', 'end', 'ref'] +
sample_names)
inclstream = concat_fields(snp_stream,
infields=snp_stream.fields[3:],
as_tuple=True)
snp_stream = FeatureStream(allsnps,
fields=['chr', 'start', 'end', 'ref'] +
sample_names)
inclstream = concat_fields(snp_stream,
infields=snp_stream.fields[3:],
as_tuple=True)
try:
annotstream = concat_fields(assembly.annot_track('CDS', chrom),
infields=['name', 'strand', 'frame'],
as_tuple=True)
annotstream = FeatureStream(
(x[:3] + (x[1:3] + x[3], ) for x in annotstream),
fields=annotstream.fields)
except:
return False
_buffer = {1: [], -1: []}
last_start = {1: -1, -1: -1}
logfile.write(" Intersection with CDS - codon changes\n")
logfile.flush()
outex = open(outexons, "a")
for x in gm_stream.intersect([inclstream, annotstream]):
# x = (chr, start,end, (alt1,alt2, , start1,end1,cds1,strand1,phase1, start2,end2,cds2,strand2,phase2 ))
# x = ('chrV',1606,1607, ('T','C (43%)', 1612,1724,'YEL077C|YEL077C',-1,0, 1712,1723,'YEL077W-A|YEL077W-A',1,0))
nsamples = len(sample_names)
chr = x[0]
pos = x[1]
rest = x[3]
refbase = rest[0]
annot = [
rest[5 * i + nsamples + 1:5 * i + 5 + nsamples + 1]
for i in range(len(rest[nsamples + 1:]) / 5)
] # list of (start,end,cds,strand,phase)
for es, ee, cds, strand, phase in annot:
if strand == 1:
shift = (pos - es - phase) % 3
elif strand == -1:
shift = (pos - ee + phase) % 3
else:
continue
codon_start = pos - shift
ref_codon = assembly.fasta_from_regions(
{chr: [[codon_start, codon_start + 3]]},
out={},
path_to_ref=genomeRef.get(chr))[0][chr][0]
info = [
chr, pos, refbase,
list(rest[1:nsamples + 1]), cds, strand,
ref_codon.upper(), shift
]
# Either the codon is the same as the previous one on this strand, or it will never be.
# Only if one codon is passed, can write its snps to a file.
if codon_start == last_start[strand]:
_buffer[strand].append(info)
else:
_write_buffer(_buffer[strand], outex)
_buffer[strand] = [info]
last_start[strand] = codon_start
for strand in [1, -1]:
_write_buffer(_buffer[strand], outex)
outex.close()
return True