def check_already_decontaminated(sample, fragment, PCR):
"""Check from the summary and output file whether decontamination has been done"""
import os
from hivwholeseq.utils.mapping import get_number_reads
if (fragment == "F4") and (sample.name in maj_contnames):
return True
fn_sum = get_decontaminate_summary_filename(sample.patient, sample.name, fragment, PCR=PCR)
fn_in = sample.get_mapped_filtered_filename(fragment, PCR=PCR, decontaminated=False)
fn_out = sample.get_mapped_filtered_filename(fragment, PCR=PCR, decontaminated=True)
if not all(map(os.path.isfile, [fn_sum, fn_in, fn_out])):
print sample.patient, sample.name, fragment, PCR
return False
n_reads_in = get_number_reads(fn_in)
n_reads_out = get_number_reads(fn_out)
(n_reads_good, n_reads_cont) = get_number_reads_summary(fn_sum)
if n_reads_out != n_reads_good:
print sample.patient, sample.name, fragment, PCR, n_reads_in, n_reads_out, n_reads_good, n_reads_cont
return False
if n_reads_good < 0.5 * n_reads_in:
print sample.patient, sample.name, fragment, PCR, n_reads_in, n_reads_out, n_reads_good, n_reads_cont
return False
return True
def check_already_decontaminated(sample, fragment, PCR):
'''Check from the summary and output file whether decontamination has been done'''
import os
from hivwholeseq.utils.mapping import get_number_reads
if (fragment == 'F4') and (sample.name in maj_contnames):
return True
fn_sum = get_decontaminate_summary_filename(sample.patient,
sample.name,
fragment,
PCR=PCR)
fn_in = sample.get_mapped_filtered_filename(fragment,
PCR=PCR,
decontaminated=False)
fn_out = sample.get_mapped_filtered_filename(fragment,
PCR=PCR,
decontaminated=True)
if not all(map(os.path.isfile, [fn_sum, fn_in, fn_out])):
print sample.patient, sample.name, fragment, PCR
return False
n_reads_in = get_number_reads(fn_in)
n_reads_out = get_number_reads(fn_out)
(n_reads_good, n_reads_cont) = get_number_reads_summary(fn_sum)
if n_reads_out != n_reads_good:
print sample.patient, sample.name, fragment, PCR, n_reads_in, n_reads_out, n_reads_good, n_reads_cont
return False
if n_reads_good < 0.5 * n_reads_in:
print sample.patient, sample.name, fragment, PCR, n_reads_in, n_reads_out, n_reads_good, n_reads_cont
return False
return True
def get_coallele_counts_from_file(bamfilename,
length,
qual_min=30,
maxreads=-1,
VERBOSE=0,
use_tests=False):
'''Get counts of join occurence of two alleles'''
from .utils.mapping import (test_read_pair_exotic_cigars,
test_read_pair_exceed_reference)
if VERBOSE >= 1:
print 'Getting coallele counts'
# Precompute conversion tables
alpha_mapping = {a: alphal.index(a) for a in alphal}
SANGER_SCORE_OFFSET = ord("!")
q_mapping = dict()
for letter in xrange(0, 255):
q_mapping[chr(letter)] = letter - SANGER_SCORE_OFFSET
if VERBOSE >= 2:
print 'Initializing matrix of cocounts'
# NOTE: we are ignoring fwd/rev and read1/2
counts = np.zeros((len(alpha), len(alpha), length, length), int)
posall = np.zeros(1000, dtype=[('pos', int), ('aind', int)])
if VERBOSE >= 2:
from hivwholeseq.utils.mapping import get_number_reads
print 'Scanning read pairs (' + str(
get_number_reads(bamfilename) // 2) + ')'
# NOTE: the reads should already be filtered of unmapped stuff at this point
with pysam.Samfile(bamfilename, 'rb') as bamfile:
for ir, reads in enumerate(pair_generator(bamfile)):
if ir == maxreads:
if VERBOSE:
print 'Max read number reached:', maxreads
break
if (VERBOSE >= 2) and (not ((ir + 1) % 10)):
if (VERBOSE == 2) and (ir + 1 != 10):
sys.stdout.write("\x1b[1A")
print(ir + 1)
if use_tests:
if test_read_pair_exotic_cigars(reads):
raise ValueError('CIGAR type ' + str(bt) +
' not recognized')
if test_read_pair_exceed_reference(reads, length):
raise ValueError('Read pair exceeds reference length of ' +
str(length))
# Temp structures
posall[:] = (-1, -1)
iall = 0
# Collect alleles
for read in reads:
alleles_ind = np.fromiter((alpha_mapping[x] for x in read.seq),
np.uint8, len(read.seq))
allqual_ind = np.fromiter((q_mapping[x] for x in read.qual),
np.uint8, len(read.qual))
pos_ref = read.pos
pos_read = 0
for (bt, bl) in read.cigar:
if bt == 1:
pos_read += bl
elif bt == 2:
# NOTE: no CIGAR can start NOR end with a deletion
qual_deletion = allqual_ind[pos_read:pos_read +
2].min()
if qual_deletion >= qual_min:
posall['pos'][iall:iall + bl] = np.arange(
pos_ref, pos_ref + bl)
posall['aind'][iall:iall + bl] = 4
iall += bl
pos_ref += bl
else:
alleles_indb = alleles_ind[pos_read:pos_read + bl]
allqual_indb = allqual_ind[pos_read:pos_read + bl]
for i in xrange(len(alpha)):
aitmp = (alleles_indb
== i) & (allqual_indb >= qual_min)
aitmp = aitmp.nonzero()[0] + pos_ref
aitmplen = len(aitmp)
posall['pos'][iall:iall + aitmplen] = aitmp
posall['aind'][iall:iall + aitmplen] = i
iall += aitmplen
pos_read += bl
pos_ref += bl
# Avoid doubles (paired reads are twice the same biological molecule)
posall.sort(order=('pos', 'aind'))
iall = (posall['pos'] != -1).nonzero()[0][0]
while iall < len(posall) - 1:
if posall['pos'][iall + 1] == posall['pos'][iall]:
# If both reads agree @ an overlap allele, take a single call
if posall['aind'][iall + 1] == posall['aind'][iall]:
posall[iall + 1] = (-1, -1)
# else, pick one at random (FIXME: pick the highest phred)
else:
ibin = np.random.randint(2)
posall[iall + ibin] = (-1, -1)
iall += 1
iall += 1
# Add allele cocounts to the matrix
# NOTE: this already takes care of the symmetry
poss = [
posall['pos'][posall['aind'] == i1]
for i1 in xrange(len(alpha))
]
for i1 in xrange(len(alpha)):
poss1 = poss[i1]
if not len(poss1):
continue
for i2 in xrange(len(alpha)):
poss2 = poss[i2]
if not len(poss2):
continue
# Raveling vodoo for efficiency
cobra = counts[i1, i2].ravel()
ind = poss1.repeat(len(poss2)) * length + np.tile(
poss2, len(poss1))
cobra[ind] += 1
return counts
def check_status(sample, step, detail=1):
'''Check for a sample a certain step of the pipeline at a certain detail'''
if detail == 1:
if step == 'premapped':
return [os.path.isfile(sample.get_premapped_filename())]
elif step == 'divided':
return [(fr, os.path.isfile(sample.get_divided_filename(fr)))
for fr in sample.regions_complete]
elif step == 'consensus':
return [(fr, os.path.isfile(sample.get_consensus_filename(fr)))
for fr in sample.regions_generic]
elif step == 'mapped':
return [
(fr,
os.path.isfile(sample.get_mapped_filename(fr,
filtered=False)))
for fr in sample.regions_generic
]
elif step == 'filtered':
return [
(fr,
os.path.isfile(sample.get_mapped_filename(fr, filtered=True)))
for fr in sample.regions_generic
]
elif step == 'mapped_initial':
return [(fr,
os.path.isfile(sample.get_mapped_to_initial_filename(fr)))
for fr in sample.regions_generic]
elif step == 'mapped_filtered':
# Check whether the mapped filtered is older than the mapped_initial
from hivwholeseq.utils.generic import modification_date
out = []
for fr in sample.regions_generic:
fn_mi = sample.get_mapped_to_initial_filename(fr)
fn_mf = sample.get_mapped_filtered_filename(fr)
if not os.path.isfile(fn_mf):
out.append((fr, False))
continue
if not os.path.isfile(fn_mi):
out.append((fr, True))
continue
md_mi = modification_date(fn_mi)
md_mf = modification_date(fn_mf)
if md_mf < md_mi:
out.append((fr, 'OLD'))
else:
out.append((fr, True))
return out
elif detail == 2:
if step in ('filtered', 'consensus'):
return check_status(sample, step, detail=3)
else:
return check_status(sample, step, detail=1)
elif detail == 3:
if step == 'premapped':
if os.path.isfile(sample.get_premapped_filename()):
return [get_number_reads(sample.get_premapped_filename())]
else:
return [False]
elif step == 'divided':
stati = []
for fr in sample.regions_complete:
fn = sample.get_divided_filename(fr)
if os.path.isfile(fn):
status = (fr, get_number_reads(fn))
else:
status = (fr, False)
stati.append(status)
return stati
elif step == 'consensus':
stati = []
for fr in sample.regions_generic:
fn = sample.get_consensus_filename(fr)
if os.path.isfile(fn):
status = (fr, len(SeqIO.read(fn, 'fasta')))
else:
status = (fr, False)
stati.append(status)
return stati
elif step == 'mapped':
stati = []
for fr in sample.regions_generic:
fn = sample.get_mapped_filename(fr, filtered=False)
if os.path.isfile(fn):
status = (fr, get_number_reads(fn))
else:
status = (fr, False)
stati.append(status)
return stati
elif step == 'filtered':
stati = []
for fr in sample.regions_generic:
fn = sample.get_mapped_filename(fr, filtered=True)
if os.path.isfile(fn):
status = (fr, get_number_reads(fn))
else:
status = (fr, False)
stati.append(status)
return stati
# TODO: add mapped_to_initial and downstream
elif step in ('mapped_initial', 'mapped_filtered'):
return check_status(sample, step, detail=1)
def filter_contamination(
bamfilename,
bamfilename_out,
contseqs,
samplename,
VERBOSE=0,
deltascore_max_self=60,
deltascore_max_other=24,
maxreads=-1,
**kwargs
):
"""Fish contaminated reads from mapped reads
The function checks for a maximal distance to the expected consensus, and only
if it's more than that it checks all other samples.
Args:
deltascore_max_self (int): the maximal delta in alignment score to the
consensus to be considered pure
deltascore_max_other (int): the maximal delta in alignment score to any other
sample to be considered a contamination
**kwargs: passed down to the pairwise alignment function
"""
import pysam
from collections import defaultdict
from operator import itemgetter
from seqanpy import align_overlap
from hivwholeseq.utils.mapping import pair_generator, get_number_reads
if "score_match" in kwargs:
score_match = kwargs["score_match"]
else:
score_match = 3
bamfilename_trash = bamfilename_out[:-4] + "_trashed.bam"
contseqs = contseqs.copy()
consseq = contseqs.pop(samplename)
if VERBOSE >= 2:
print "Scanning reads (" + str(get_number_reads(bamfilename) // 2) + ")"
with pysam.Samfile(bamfilename, "rb") as bamfile:
with pysam.Samfile(bamfilename_out, "wb", template=bamfile) as bamfileout, pysam.Samfile(
bamfilename_trash, "wb", template=bamfile
) as bamfiletrash:
n_good = 0
n_cont = defaultdict(int)
for irp, reads in enumerate(pair_generator(bamfile)):
if irp == maxreads:
break
if VERBOSE >= 2:
if not ((irp + 1) % 100):
if not ((irp + 1) == 100):
sys.stdout.write("\x1b[1A")
print irp + 1
for read in reads:
# Look for distance to the own consensus, it that's small move on
alignments_read = {}
deltas_read = {}
(score, alis1, alis2) = align_overlap(consseq, read.seq, **kwargs)
(alis1, alis2) = trim_align_overlap((alis1, alis2))
scoremax = len(alis1) * score_match
delta_read = scoremax - score
deltas_read[samplename] = delta_read
alignments_read[samplename] = (alis1, alis2)
if delta_read <= deltascore_max_self:
if VERBOSE >= 4:
print "Read is very close to its own consensus", scoremax, score, delta_read
pretty_print_pairwise_ali([alis1, alis2], width=90, name1="ref", name2="read")
continue
# Otherwise, move on to all other sequences and find the neighbour
for contname, contseq in contseqs.iteritems():
(score, ali1, ali2) = align_overlap(contseq, read.seq, **kwargs)
(ali1, ali2) = trim_align_overlap((ali1, ali2))
scoremax = len(ali1) * score_match
delta_read = scoremax - score
deltas_read[contname] = delta_read
alignments_read[contname] = (ali1, ali2)
if VERBOSE >= 5:
print samplename
for key, d in deltas_read.iteritems():
print key, d
(contname, delta_read) = min(deltas_read.iteritems(), key=itemgetter(1))
# Again, the correct consensus has precedence
if deltas_read[samplename] == delta_read:
contname = samplename
(ali1, ali2) = alignments_read[contname]
# The read may be closest to its own consensus, if not very close
if contname == samplename:
if VERBOSE >= 4:
print "Read is closest to its consensus", scoremax, score, delta_read
pretty_print_pairwise_ali([ali1, ali2], width=90, name1="ref", name2="read")
# The read may come from another consensus (contamination)
elif delta_read <= deltascore_max_other:
n_cont[contname] += 1
bamfiletrash.write(reads[0])
bamfiletrash.write(reads[1])
if VERBOSE >= 2:
print "Contaminated read found! Good:", n_good, "cont:", sum(
n_cont.itervalues()
), "sources:", n_cont
if VERBOSE >= 3:
print "Read is contaminated by", contname, scoremax, score, delta_read
pretty_print_pairwise_ali([alis1, alis2], width=90, name1="self", name2="read")
print ""
pretty_print_pairwise_ali([ali1, ali2], width=90, name1="ref", name2="read")
if VERBOSE >= 2:
print ""
break
# Finally, the read is not really close to anything: accept
else:
if VERBOSE >= 4:
print "Read is close to nothing really", scoremax, score, delta_read
pretty_print_pairwise_ali([ali1, ali2], width=90, name1="ref", name2="read")
else:
n_good += 1
bamfileout.write(reads[0])
bamfileout.write(reads[1])
n_cont = dict(n_cont)
return (n_good, n_cont)
def print_info_genomewide(p, title, name, method, VERBOSE=0, require_all=True):
'''Pretty printer for patient pipeline info'''
mod_dates = p.mod_dates
def check_requisite_genomewide(md,
name_requisite,
samplename,
mod_dates,
require_all=True):
'''Check requisites for genomewide observables'''
stati = []
fragments = ['F' + str(i + 1) for i in xrange(6)]
for fragment in fragments:
if (name_requisite, fragment, samplename) not in mod_dates:
stati.append('MISS')
elif md < mod_dates[(name_requisite, fragment, samplename)]:
stati.append('OLD')
else:
stati.append('OK')
if 'OLD' in stati:
return 'OLD'
else:
if require_all:
if 'MISS' in stati:
return 'MISS'
else:
return 'OK'
else:
if 'OK' in stati:
return 'OK'
else:
return 'MISS'
def check_contamination_genomewide(sample):
'''Check whether any of the fragment samples is contaminated'''
fragments = ['F' + str(i + 1) for i in xrange(6)]
for fragment in fragments:
if 'contaminated' in sample[fragment]:
return True
return False
import os, sys
from hivwholeseq.patients.samples import SamplePat
# NOTE: this function is used to check both entire patients and single samples
if isinstance(p, SamplePat):
sample_iter = [(p.name, p)]
else:
sample_iter = p.samples.iterrows()
stati = set()
line = ('{:<' + str(title_len) + '}').format(title + ':')
print line
for samplename, sample in sample_iter:
sample = SamplePat(sample)
title = sample.name
line = ('{:<' + str(title_len) + '}').format(title + ':')
if isinstance(method, basestring) and hasattr(sample, method):
fun = getattr(sample, method)
fn = fun('genomewide')
else:
fn = method(sample.patient, samplename, 'genomewide')
if os.path.isfile(fn):
md = modification_date(fn)
mod_dates[(name, 'genomewide', samplename)] = md
if name is None:
status = 'OK'
elif check_contamination_genomewide(sample):
status = 'CONT'
else:
status = check_requisite_genomewide(md,
name,
samplename,
mod_dates,
require_all=require_all)
else:
status = 'MISS'
# Check the number of reads if requested
if (status == 'OK') and (fn[-3:] == 'bam') and (VERBOSE >= 3):
status = str(get_number_reads(fn))
stati.add(status)
line = line + ('{:<' + str(cell_len) + '}').format(status)
print line
if 'OLD' in stati:
raise ValueError('OLD status found')
def print_info(p, title, name, method, name_requisite=None, VERBOSE=0):
'''Pretty printer for patient pipeline info'''
import os, sys
from hivwholeseq.patients.samples import SamplePat
from hivwholeseq.utils.mapping import get_number_reads
mod_dates = p.mod_dates
# NOTE: this function is used to check both entire patients and single samples
if isinstance(p, SamplePat):
sample_iter = [(p.name, p)]
else:
sample_iter = p.samples.iterrows()
fragments = ['F' + str(i + 1) for i in xrange(6)]
stati = set()
line = ('{:<' + str(title_len) + '}').format(title + ':')
print line
for samplename, sample in sample_iter:
sample = SamplePat(sample)
title = sample.name
line = ('{:<' + str(title_len) + '}').format(title + ':')
for fragment in fragments:
if isinstance(method, basestring) and hasattr(sample, method):
fun = getattr(sample, method)
fn = fun(fragment)
else:
fn = method(sample.patient, samplename, fragment)
if os.path.isfile(fn):
md = modification_date(fn)
mod_dates[(name, fragment, samplename)] = md
if name_requisite is None:
status = 'OK'
elif ((name_requisite, fragment, samplename) in mod_dates):
if md > mod_dates[(name_requisite, fragment, samplename)]:
status = 'OK'
else:
status = 'OLD'
print fn, md, mod_dates[(name_requisite, fragment,
samplename)]
elif ((name_requisite, fragment) in mod_dates):
if md > mod_dates[(name_requisite, fragment)]:
status = 'OK'
else:
status = 'OLD'
# NOTE: on Nov 13, 2014 I updated the mod dates of all
# references by mistake, without actually changing the
# sequences (ironically, probably testing a backup system
# for the refs themselves). So if the requisite is a ref
# seq and the date is this one, it's OK
if ((name_requisite == 'reference') and
mod_dates[(name_requisite, fragment)].date() == \
datetime.date(2014, 11, 13)):
status = 'OK'
elif 'contaminated' in sample[fragment]:
status = 'CONT'
else:
status = 'ERROR'
else:
status = 'MISS'
# Check the number of reads if requested
if (status == 'OK') and (fn[-3:] == 'bam') and (VERBOSE >= 3):
status = str(get_number_reads(fn))
stati.add(status)
line = line+fragment+': '+\
('{:>'+str(cell_len - len(fragment) - 1)+'}').format(status)+' '
print line
if 'OLD' in stati:
raise ValueError('OLD status found')
def filter_contamination(bamfilename,
bamfilename_out,
contseqs,
samplename,
VERBOSE=0,
deltascore_max_self=60,
deltascore_max_other=24,
maxreads=-1,
**kwargs):
'''Fish contaminated reads from mapped reads
The function checks for a maximal distance to the expected consensus, and only
if it's more than that it checks all other samples.
Args:
deltascore_max_self (int): the maximal delta in alignment score to the
consensus to be considered pure
deltascore_max_other (int): the maximal delta in alignment score to any other
sample to be considered a contamination
**kwargs: passed down to the pairwise alignment function
'''
import pysam
from collections import defaultdict
from operator import itemgetter
from seqanpy import align_overlap
from hivwholeseq.utils.mapping import pair_generator, get_number_reads
if 'score_match' in kwargs:
score_match = kwargs['score_match']
else:
score_match = 3
bamfilename_trash = bamfilename_out[:-4] + '_trashed.bam'
contseqs = contseqs.copy()
consseq = contseqs.pop(samplename)
if VERBOSE >= 2:
print 'Scanning reads (' + str(
get_number_reads(bamfilename) // 2) + ')'
with pysam.Samfile(bamfilename, 'rb') as bamfile:
with pysam.Samfile(bamfilename_out, 'wb', template=bamfile) as bamfileout, \
pysam.Samfile(bamfilename_trash, 'wb', template=bamfile) as bamfiletrash:
n_good = 0
n_cont = defaultdict(int)
for irp, reads in enumerate(pair_generator(bamfile)):
if irp == maxreads:
break
if VERBOSE >= 2:
if not ((irp + 1) % 100):
if not ((irp + 1) == 100):
sys.stdout.write('\x1b[1A')
print irp + 1
for read in reads:
# Look for distance to the own consensus, it that's small move on
alignments_read = {}
deltas_read = {}
(score, alis1,
alis2) = align_overlap(consseq, read.seq, **kwargs)
(alis1, alis2) = trim_align_overlap((alis1, alis2))
scoremax = len(alis1) * score_match
delta_read = scoremax - score
deltas_read[samplename] = delta_read
alignments_read[samplename] = (alis1, alis2)
if delta_read <= deltascore_max_self:
if VERBOSE >= 4:
print 'Read is very close to its own consensus', scoremax, score, delta_read
pretty_print_pairwise_ali([alis1, alis2],
width=90,
name1='ref',
name2='read')
continue
# Otherwise, move on to all other sequences and find the neighbour
for contname, contseq in contseqs.iteritems():
(score, ali1,
ali2) = align_overlap(contseq, read.seq, **kwargs)
(ali1, ali2) = trim_align_overlap((ali1, ali2))
scoremax = len(ali1) * score_match
delta_read = scoremax - score
deltas_read[contname] = delta_read
alignments_read[contname] = (ali1, ali2)
if VERBOSE >= 5:
print samplename
for key, d in deltas_read.iteritems():
print key, d
(contname, delta_read) = min(deltas_read.iteritems(),
key=itemgetter(1))
# Again, the correct consensus has precedence
if deltas_read[samplename] == delta_read:
contname = samplename
(ali1, ali2) = alignments_read[contname]
# The read may be closest to its own consensus, if not very close
if contname == samplename:
if VERBOSE >= 4:
print 'Read is closest to its consensus', scoremax, score, delta_read
pretty_print_pairwise_ali([ali1, ali2],
width=90,
name1='ref',
name2='read')
# The read may come from another consensus (contamination)
elif (delta_read <= deltascore_max_other):
n_cont[contname] += 1
bamfiletrash.write(reads[0])
bamfiletrash.write(reads[1])
if VERBOSE >= 2:
print 'Contaminated read found! Good:', n_good, 'cont:', sum(
n_cont.itervalues()), 'sources:', n_cont
if VERBOSE >= 3:
print 'Read is contaminated by', contname, scoremax, score, delta_read
pretty_print_pairwise_ali([alis1, alis2],
width=90,
name1='self',
name2='read')
print ''
pretty_print_pairwise_ali([ali1, ali2],
width=90,
name1='ref',
name2='read')
if VERBOSE >= 2:
print ''
break
# Finally, the read is not really close to anything: accept
else:
if VERBOSE >= 4:
print 'Read is close to nothing really', scoremax, score, delta_read
pretty_print_pairwise_ali([ali1, ali2],
width=90,
name1='ref',
name2='read')
else:
n_good += 1
bamfileout.write(reads[0])
bamfileout.write(reads[1])
n_cont = dict(n_cont)
return (n_good, n_cont)
def get_coallele_counts_from_file(bamfilename, length, qual_min=30,
maxreads=-1, VERBOSE=0,
use_tests=False):
'''Get counts of join occurence of two alleles'''
from .utils.mapping import (test_read_pair_exotic_cigars,
test_read_pair_exceed_reference)
if VERBOSE >= 1:
print 'Getting coallele counts'
# Precompute conversion tables
alpha_mapping = {a: alphal.index(a) for a in alphal}
SANGER_SCORE_OFFSET = ord("!")
q_mapping = dict()
for letter in xrange(0, 255):
q_mapping[chr(letter)] = letter - SANGER_SCORE_OFFSET
if VERBOSE >= 2:
print 'Initializing matrix of cocounts'
# NOTE: we are ignoring fwd/rev and read1/2
counts = np.zeros((len(alpha), len(alpha), length, length), int)
posall = np.zeros(1000, dtype=[('pos', int), ('aind', int)])
if VERBOSE >= 2:
from hivwholeseq.utils.mapping import get_number_reads
print 'Scanning read pairs ('+str(get_number_reads(bamfilename) // 2)+')'
# NOTE: the reads should already be filtered of unmapped stuff at this point
with pysam.Samfile(bamfilename, 'rb') as bamfile:
for ir, reads in enumerate(pair_generator(bamfile)):
if ir == maxreads:
if VERBOSE:
print 'Max read number reached:', maxreads
break
if (VERBOSE >= 2) and (not ((ir +1) % 10)):
if (VERBOSE == 2) and (ir + 1 != 10):
sys.stdout.write("\x1b[1A")
print (ir+1)
if use_tests:
if test_read_pair_exotic_cigars(reads):
raise ValueError('CIGAR type '+str(bt)+' not recognized')
if test_read_pair_exceed_reference(reads, length):
raise ValueError('Read pair exceeds reference length of '+str(length))
# Temp structures
posall[:] = (-1, -1)
iall = 0
# Collect alleles
for read in reads:
alleles_ind = np.fromiter((alpha_mapping[x] for x in read.seq),
np.uint8, len(read.seq))
allqual_ind = np.fromiter((q_mapping[x] for x in read.qual),
np.uint8, len(read.qual))
pos_ref = read.pos
pos_read = 0
for (bt, bl) in read.cigar:
if bt == 1:
pos_read += bl
elif bt == 2:
# NOTE: no CIGAR can start NOR end with a deletion
qual_deletion = allqual_ind[pos_read: pos_read + 2].min()
if qual_deletion >= qual_min:
posall['pos'][iall: iall + bl] = np.arange(pos_ref,
pos_ref + bl)
posall['aind'][iall: iall + bl] = 4
iall += bl
pos_ref += bl
else:
alleles_indb = alleles_ind[pos_read: pos_read + bl]
allqual_indb = allqual_ind[pos_read: pos_read + bl]
for i in xrange(len(alpha)):
aitmp = (alleles_indb == i) & (allqual_indb >= qual_min)
aitmp = aitmp.nonzero()[0] + pos_ref
aitmplen = len(aitmp)
posall['pos'][iall: iall + aitmplen] = aitmp
posall['aind'][iall: iall + aitmplen] = i
iall += aitmplen
pos_read += bl
pos_ref += bl
# Avoid doubles (paired reads are twice the same biological molecule)
posall.sort(order=('pos', 'aind'))
iall = (posall['pos'] != -1).nonzero()[0][0]
while iall < len(posall) - 1:
if posall['pos'][iall + 1] == posall['pos'][iall]:
# If both reads agree @ an overlap allele, take a single call
if posall['aind'][iall + 1] == posall['aind'][iall]:
posall[iall + 1] = (-1, -1)
# else, pick one at random (FIXME: pick the highest phred)
else:
ibin = np.random.randint(2)
posall[iall + ibin] = (-1, -1)
iall += 1
iall += 1
# Add allele cocounts to the matrix
# NOTE: this already takes care of the symmetry
poss = [posall['pos'][posall['aind'] == i1] for i1 in xrange(len(alpha))]
for i1 in xrange(len(alpha)):
poss1 = poss[i1]
if not len(poss1):
continue
for i2 in xrange(len(alpha)):
poss2 = poss[i2]
if not len(poss2):
continue
# Raveling vodoo for efficiency
cobra = counts[i1, i2].ravel()
ind = poss1.repeat(len(poss2)) * length + np.tile(poss2, len(poss1))
cobra[ind] += 1
return counts
def check_premap(data_folder, adaID, fragments, seq_run, samplename,
qual_min=30, match_len_min=10,
maxreads=-1, VERBOSE=0,
savefig=True,
title=None):
'''Check premap to reference: coverage, etc.'''
refseq = SeqIO.read(get_reference_premap_filename(data_folder, adaID), 'fasta')
# FIXME: do this possibly better than parsing the description!
try:
fields = refseq.description.split()
refseq_start = int(fields[fields.index('(indices') - 3])
except ValueError:
refseq_start = 550
fragpos_filename = get_fragment_positions_filename(data_folder, adaID)
if os.path.isfile(fragpos_filename):
# Load the fragment positions, considering mixed fragments (e.g. F5a+b)
fragtmp = []
postmp = []
with open(fragpos_filename, 'r') as f:
f.readline() #HEADER
for line in f:
fields = line[:-1].split('\t')
fragtmp.append(fields[0])
if 'inner' not in fields[1]:
postmp.append([fields[1], fields[4]])
else:
start = int(fields[1].split(',')[1].split(': ')[1].rstrip('}'))
end = int(fields[4].split(',')[1].split(': ')[1].rstrip('}'))
postmp.append([start, end])
postmp = np.array(postmp, int)
# NOTE: In a lot of old files, it says F3o instead of F3ao
if 'F3o' in fragtmp:
fragtmp[fragtmp.index('F3o')] = 'F3ao'
elif 'F3i' in fragtmp:
fragtmp[fragtmp.index('F3i')] = 'F3ai'
frags_pos = np.array([postmp[fragtmp.index(fr)] for fr in fragments], int).T
else:
frags_pos = None
frags_pos_out = None
# Open BAM and scan reads
input_filename = get_premapped_filename(data_folder, adaID, type='bam')
if not os.path.isfile(input_filename):
if VERBOSE:
print 'Premapped BAM file not found'
return (None, None)
# Count reads if requested
n_reads = get_number_reads(input_filename)
if VERBOSE:
print 'N. of reads:', n_reads
# Get counts
counts, inserts = get_allele_counts_insertions_from_file_unfiltered(input_filename,
len(refseq),
qual_min=qual_min,
match_len_min=match_len_min,
maxreads=maxreads,
VERBOSE=VERBOSE)
# Plot results
if title is None:
title=', '.join(['run '+seq_run+' '+adaID,
'sample '+samplename,
'reads '+str(min(maxreads, n_reads))+'/'+str(n_reads),
])
plot_coverage(counts,
offset_x=refseq_start,
frags_pos=frags_pos,
frags_pos_out=frags_pos_out,
title=title)
if savefig:
from hivwholeseq.sequencing.adapter_info import foldername_adapter
plt.savefig(data_folder+foldername_adapter(adaID)+'figures/coverage_premapped_'+samplename+'.png')
return (counts, inserts)
def print_info_genomewide(p, title, name, method, VERBOSE=0, require_all=True):
'''Pretty printer for patient pipeline info'''
mod_dates = p.mod_dates
def check_requisite_genomewide(md, name_requisite, samplename, mod_dates,
require_all=True):
'''Check requisites for genomewide observables'''
stati = []
fragments=['F'+str(i+1) for i in xrange(6)]
for fragment in fragments:
if (name_requisite, fragment, samplename) not in mod_dates:
stati.append('MISS')
elif md < mod_dates[(name_requisite, fragment, samplename)]:
stati.append('OLD')
else:
stati.append('OK')
if 'OLD' in stati:
return 'OLD'
else:
if require_all:
if 'MISS' in stati:
return 'MISS'
else:
return 'OK'
else:
if 'OK' in stati:
return 'OK'
else:
return 'MISS'
def check_contamination_genomewide(sample):
'''Check whether any of the fragment samples is contaminated'''
fragments=['F'+str(i+1) for i in xrange(6)]
for fragment in fragments:
if 'contaminated' in sample[fragment]:
return True
return False
import os, sys
from hivwholeseq.patients.samples import SamplePat
# NOTE: this function is used to check both entire patients and single samples
if isinstance(p, SamplePat):
sample_iter = [(p.name, p)]
else:
sample_iter = p.samples.iterrows()
stati = set()
line = ('{:<'+str(title_len)+'}').format(title+':')
print line
for samplename, sample in sample_iter:
sample = SamplePat(sample)
title = sample.name
line = ('{:<'+str(title_len)+'}').format(title+':')
if isinstance(method, basestring) and hasattr(sample, method):
fun = getattr(sample, method)
fn = fun('genomewide')
else:
fn = method(sample.patient, samplename, 'genomewide')
if os.path.isfile(fn):
md = modification_date(fn)
mod_dates[(name, 'genomewide', samplename)] = md
if name is None:
status = 'OK'
elif check_contamination_genomewide(sample):
status = 'CONT'
else:
status = check_requisite_genomewide(md, name, samplename, mod_dates,
require_all=require_all)
else:
status = 'MISS'
# Check the number of reads if requested
if (status == 'OK') and (fn[-3:] == 'bam') and (VERBOSE >= 3):
status = str(get_number_reads(fn))
stati.add(status)
line = line + ('{:<'+str(cell_len)+'}').format(status)
print line
if 'OLD' in stati:
raise ValueError('OLD status found')
def print_info(p, title, name, method, name_requisite=None, VERBOSE=0):
'''Pretty printer for patient pipeline info'''
import os, sys
from hivwholeseq.patients.samples import SamplePat
from hivwholeseq.utils.mapping import get_number_reads
mod_dates = p.mod_dates
# NOTE: this function is used to check both entire patients and single samples
if isinstance(p, SamplePat):
sample_iter = [(p.name, p)]
else:
sample_iter = p.samples.iterrows()
fragments=['F'+str(i+1) for i in xrange(6)]
stati = set()
line = ('{:<'+str(title_len)+'}').format(title+':')
print line
for samplename, sample in sample_iter:
sample = SamplePat(sample)
title = sample.name
line = ('{:<'+str(title_len)+'}').format(title+':')
for fragment in fragments:
if isinstance(method, basestring) and hasattr(sample, method):
fun = getattr(sample, method)
fn = fun(fragment)
else:
fn = method(sample.patient, samplename, fragment)
if os.path.isfile(fn):
md = modification_date(fn)
mod_dates[(name, fragment, samplename)] = md
if name_requisite is None:
status = 'OK'
elif ((name_requisite, fragment, samplename) in mod_dates):
if md > mod_dates[(name_requisite, fragment, samplename)]:
status = 'OK'
else:
status = 'OLD'
print fn, md, mod_dates[(name_requisite, fragment, samplename)]
elif ((name_requisite, fragment) in mod_dates):
if md > mod_dates[(name_requisite, fragment)]:
status = 'OK'
else:
status = 'OLD'
# NOTE: on Nov 13, 2014 I updated the mod dates of all
# references by mistake, without actually changing the
# sequences (ironically, probably testing a backup system
# for the refs themselves). So if the requisite is a ref
# seq and the date is this one, it's OK
if ((name_requisite == 'reference') and
mod_dates[(name_requisite, fragment)].date() == \
datetime.date(2014, 11, 13)):
status = 'OK'
elif 'contaminated' in sample[fragment]:
status = 'CONT'
else:
status = 'ERROR'
else:
status = 'MISS'
# Check the number of reads if requested
if (status == 'OK') and (fn[-3:] == 'bam') and (VERBOSE >= 3):
status = str(get_number_reads(fn))
stati.add(status)
line = line+fragment+': '+\
('{:>'+str(cell_len - len(fragment) - 1)+'}').format(status)+' '
print line
if 'OLD' in stati:
raise ValueError('OLD status found')
def check_premap(data_folder,
adaID,
fragments,
seq_run,
samplename,
qual_min=30,
match_len_min=10,
maxreads=-1,
VERBOSE=0,
savefig=True,
title=None):
'''Check premap to reference: coverage, etc.'''
refseq = SeqIO.read(get_reference_premap_filename(data_folder, adaID),
'fasta')
# FIXME: do this possibly better than parsing the description!
try:
fields = refseq.description.split()
refseq_start = int(fields[fields.index('(indices') - 3])
except ValueError:
refseq_start = 550
fragpos_filename = get_fragment_positions_filename(data_folder, adaID)
if os.path.isfile(fragpos_filename):
# Load the fragment positions, considering mixed fragments (e.g. F5a+b)
fragtmp = []
postmp = []
with open(fragpos_filename, 'r') as f:
f.readline() #HEADER
for line in f:
fields = line[:-1].split('\t')
fragtmp.append(fields[0])
if 'inner' not in fields[1]:
postmp.append([fields[1], fields[4]])
else:
start = int(
fields[1].split(',')[1].split(': ')[1].rstrip('}'))
end = int(
fields[4].split(',')[1].split(': ')[1].rstrip('}'))
postmp.append([start, end])
postmp = np.array(postmp, int)
# NOTE: In a lot of old files, it says F3o instead of F3ao
if 'F3o' in fragtmp:
fragtmp[fragtmp.index('F3o')] = 'F3ao'
elif 'F3i' in fragtmp:
fragtmp[fragtmp.index('F3i')] = 'F3ai'
frags_pos = np.array([postmp[fragtmp.index(fr)] for fr in fragments],
int).T
else:
frags_pos = None
frags_pos_out = None
# Open BAM and scan reads
input_filename = get_premapped_filename(data_folder, adaID, type='bam')
if not os.path.isfile(input_filename):
if VERBOSE:
print 'Premapped BAM file not found'
return (None, None)
# Count reads if requested
n_reads = get_number_reads(input_filename)
if VERBOSE:
print 'N. of reads:', n_reads
# Get counts
counts, inserts = get_allele_counts_insertions_from_file_unfiltered(
input_filename,
len(refseq),
qual_min=qual_min,
match_len_min=match_len_min,
maxreads=maxreads,
VERBOSE=VERBOSE)
# Plot results
if title is None:
title = ', '.join([
'run ' + seq_run + ' ' + adaID,
'sample ' + samplename,
'reads ' + str(min(maxreads, n_reads)) + '/' + str(n_reads),
])
plot_coverage(counts,
offset_x=refseq_start,
frags_pos=frags_pos,
frags_pos_out=frags_pos_out,
title=title)
if savefig:
from hivwholeseq.sequencing.adapter_info import foldername_adapter
plt.savefig(data_folder + foldername_adapter(adaID) +
'figures/coverage_premapped_' + samplename + '.png')
return (counts, inserts)