def compress(outdir):
for module in ['pan_genomes', 'rep_genomes']:
for species in os.listdir('%s/%s' % (outdir, module)):
indir = '%s/%s/%s' % (outdir, module, species)
for file in os.listdir(indir):
inpath = '%s/%s' % (indir, file)
if inpath.split('.')[-1] != 'gz':
outfile = utility.iopen('%s/%s.gz' % (indir, file), 'w')
for line in utility.iopen(inpath):
outfile.write(line)
outfile.close()
os.remove(inpath)
def build_pangenome_db(args, species):
""" Build FASTA and BT2 database from pangene species centroids """
import Bio.SeqIO
# fasta database
outdir = '/'.join([args['outdir'], 'genes/temp'])
pangenome_fasta = open('/'.join([outdir, 'pangenomes.fa']), 'w')
pangenome_map = open('/'.join([outdir, 'pangenomes.map']), 'w')
db_stats = {'total_length':0, 'total_seqs':0, 'species':0}
for sp in species.values():
db_stats['species'] += 1
infile = utility.iopen(sp.paths['centroids.ffn'])
for r in Bio.SeqIO.parse(infile, 'fasta'):
pangenome_fasta.write('>%s\n%s\n' % (r.id, str(r.seq).upper()))
pangenome_map.write('%s\t%s\n' % (r.id, sp.id))
db_stats['total_length'] += len(r.seq)
db_stats['total_seqs'] += 1
infile.close()
pangenome_fasta.close()
pangenome_map.close()
# print out database stats
print(" total species: %s" % db_stats['species'])
print(" total genes: %s" % db_stats['total_seqs'])
print(" total base-pairs: %s" % db_stats['total_length'])
# bowtie2 database
inpath = '/'.join([outdir, 'pangenomes.fa'])
outpath = '/'.join([outdir, 'pangenomes'])
command = ' '.join([args['bowtie2-build'], inpath, outpath])
args['log'].write('command: '+command+'\n')
process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
def species_pileup(args, species_id, contigs):
# Set global variables for read filtering
global global_args # need global for keep_read function
global_args = args
# summary stats
global aln_stats
aln_stats = {
'genome_length': 0,
'total_depth': 0,
'covered_bases': 0,
'aligned_reads': 0,
'mapped_reads': 0
}
# open outfiles
out_path = '%s/snps/output/%s.snps.gz' % (args['outdir'], species_id)
out_file = utility.iopen(out_path, 'w')
header = [
'ref_id', 'ref_pos', 'ref_allele', 'depth', 'count_a', 'count_c',
'count_g', 'count_t'
]
out_file.write('\t'.join(header) + '\n')
# compute coverage
bampath = '%s/snps/temp/genomes.bam' % args['outdir']
with pysam.AlignmentFile(bampath, 'rb') as bamfile:
for contig_id in sorted(list(contigs.keys())):
contig = contigs[contig_id]
if contig.species_id != species_id:
continue
counts = bamfile.count_coverage(contig.id,
start=0,
end=contig.length,
quality_threshold=args['baseq'],
read_callback=keep_read)
for i in range(0, contig.length):
ref_pos = i + 1
ref_allele = contig.seq[i]
depth = sum([counts[_][i] for _ in range(4)])
count_a = counts[0][i]
count_c = counts[1][i]
count_g = counts[2][i]
count_t = counts[3][i]
row = [
contig.id, ref_pos, ref_allele, depth, count_a, count_c,
count_g, count_t
]
out_file.write('\t'.join([str(_) for _ in row]) + '\n')
aln_stats['genome_length'] += 1
aln_stats['total_depth'] += depth
if depth > 0: aln_stats['covered_bases'] += 1
out_file.close()
return (species_id, aln_stats)
def format_vcf(args):
""" Format vcf files to snp files and fill in missing positions """
inpath = os.path.join(args['outdir'], 'snps/temp/genomes.map')
ref_to_species = utility.read_ref_to_cluster(inpath)
for species_id in set(ref_to_species.values()):
# open outfile
outpath = '/'.join(
[args['outdir'],
'snps/output/%s.snps.gz' % species_id])
outfile = utility.iopen(outpath, 'w')
write_snp_record(outfile, header=True)
# read sorted reference
ref = read_ref_bases(args, species_id)
ref_index = 0
ref_length = len(ref)
# write formatted records
vcf_path = '/'.join(
[args['outdir'],
'snps/temp/vcf/%s.vcf' % species_id])
for snp in parse_vcf(vcf_path): # loop over formatted records from vcf
while [snp['ref_id'], snp['ref_pos']
] != ref[ref_index][0:2]: # fill in missing snp positions
write_snp_record(outfile, None,
ref[ref_index]) # write missing record
ref_index += 1
write_snp_record(outfile, snp, None) # write present record
ref_index += 1
while ref_index < ref_length: # fill in trailing snps
write_snp_record(outfile, None,
ref[ref_index]) # write trailing record
ref_index += 1
def write_species_info(args, species):
outfile = utility.iopen('%s/species_info.txt' % args['outdir'], 'w')
header = ['species_id', 'rep_genome', 'count_genomes']
outfile.write('\t'.join(header) + '\n')
for sp in species:
values = [str(_) for _ in [sp.id, sp.rep_genome, sp.ngenomes]]
outfile.write('\t'.join(values) + '\n')
def main():
""" Run main pipeline """
args = parse_args()
reads = 0
bp = 0
for inpath in args['input']:
infile = utility.iopen(inpath)
for name, seq, qual in readfq(infile):
seq_len = len(seq)
if args['read_length']: # trim/filter reads
if seq_len < args['read_length']:
continue
else:
seq = seq[0:args['read_length']]
seq_len = len(seq)
sys.stdout.write('>%s_%s\n%s\n' % (name, seq_len, seq))
reads += 1
bp += seq_len
if reads == args['max_reads']:
sys.stderr.write(
'%s\t%s' %
(reads, bp)) # write number of reads, bp to stderr
return
sys.stderr.write('%s\t%s' %
(reads, bp)) # write number of reads, bp to stderr
def write_results(args, species, genes):
""" Write results to disk """
# open outfiles for each species_id
header = ['gene_id', 'count_reads', 'coverage', 'copy_number']
for sp in species.values():
path = '/'.join([args['outdir'], 'genes/output/%s.genes.gz' % sp.id])
sp.out = utility.iopen(path, 'w')
sp.out.write('\t'.join(header)+'\n')
# write to output files
for gene_id in sorted(genes):
gene = genes[gene_id]
sp = species[gene.species_id]
values = [gene.id, gene.reads, gene.depth, gene.copies]
sp.out.write('\t'.join([str(_) for _ in values])+'\n')
# close output files
for sp in species.values():
sp.out.close()
# summary stats
path = '/'.join([args['outdir'], 'genes/summary.txt'])
file = open(path, 'w')
header = ['species_id', 'pangenome_size', 'covered_genes', 'fraction_covered', 'mean_coverage', 'marker_coverage', 'count_reads']
file.write('\t'.join(header)+'\n')
for sp in species.values():
values = [sp.id, sp.pangenome_size, sp.covered_genes, sp.fraction_covered, sp.mean_coverage, sp.marker_coverage, sp.reads]
file.write('\t'.join([str(_) for _ in values])+'\n')
file.close()
def build_pangenome_db(args, genome_clusters):
""" Build FASTA and BT2 database from pangene cluster centroids """
import Bio.SeqIO
# fasta database
outdir = '/'.join([args['outdir'], 'genes/temp'])
pangenome_fasta = open('/'.join([outdir, 'pangenomes.fa']), 'w')
pangenome_map = open('/'.join([outdir, 'pangenome.map']), 'w')
db_stats = {'total_length':0, 'total_seqs':0, 'genome_clusters':0}
for species_id in genome_clusters:
db_stats['genome_clusters'] += 1
inpath = '/'.join([args['db'], 'genome_clusters', species_id, 'pangenome.fa.gz'])
infile = utility.iopen(inpath)
for r in Bio.SeqIO.parse(infile, 'fasta'):
genome_id = '.'.join(r.id.split('.')[0:2])
if not args['tax_mask'] or genome_id not in args['tax_mask']:
pangenome_fasta.write('>%s\n%s\n' % (r.id, str(r.seq)))
pangenome_map.write('%s\t%s\n' % (r.id, species_id))
db_stats['total_length'] += len(r.seq)
db_stats['total_seqs'] += 1
pangenome_fasta.close()
pangenome_map.close()
# print out database stats
print(" total species: %s" % db_stats['genome_clusters'])
print(" total genes: %s" % db_stats['total_seqs'])
print(" total base-pairs: %s" % db_stats['total_length'])
# bowtie2 database
inpath = '/'.join([outdir, 'pangenomes.fa'])
outpath = '/'.join([outdir, 'pangenomes'])
command = ' '.join([args['bowtie2-build'], inpath, outpath])
args['log'].write('command: '+command+'\n')
process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
def compute_pangenome_coverage(args):
""" Compute coverage of pangenome for species_id and write results to disk """
# map ref_id to species_id
ref_to_cluster = {}
for line in open('/'.join([args['outdir'], 'genes/temp/pangenome.map'])):
ref_id, species_id = line.rstrip().split()
ref_to_cluster[ref_id] = species_id
# open outfiles for each species_id
outfiles = {}
genome_clusters = set(ref_to_cluster.values())
for species_id in genome_clusters:
outpath = '/'.join([args['outdir'], 'genes/output/%s.genes.gz' % species_id])
outfiles[species_id] = utility.iopen(outpath, 'w')
outfiles[species_id].write('\t'.join(['gene_id', 'coverage', 'copy_number'])+'\n')
# parse bam into cov files for each species_id
ref_to_cov = count_mapped_bp(args)
# compute normalization factor
cluster_to_norm = compute_phyeco_cov(args, genome_clusters, ref_to_cov, ref_to_cluster)
# write to output files
for ref_id in sorted(ref_to_cov):
cov = ref_to_cov[ref_id]
species_id = ref_to_cluster[ref_id]
outfile = outfiles[species_id]
normcov = cov/cluster_to_norm[species_id] if cluster_to_norm[species_id] > 0 else 0.0
outfile.write('\t'.join([str(x) for x in [ref_id, cov, normcov]])+'\n')
def write_readme(self):
""" Concatenate all genes from pangenome into sequence file """
file = utility.iopen('%s/readme.txt' % self.dir, 'w')
file.write("""
Description and statistics for pan-genome files
Summary Statistics
############
Genomes: %(genomes)s
Genes: %(genes)s
Gene clusters (95%% identity): %(centroids_95)s
Gene clusters (90%% identity): %(centroids_90)s
Gene clusters (85%% identity): %(centroids_85)s
Gene clusters (80%% identity): %(centroids_80)s
Gene clusters (75%% identity): %(centroids_75)s
Output files
############
genes.ffn
all genes from specified genomes
centroids.ffn
gene sequences from 95%% identity gene clusters
used for recruiting metagenomic reads
gene_info.txt
information for all genes from genes.ffn
the fields centroid_{95,90,95,80,75} indicate mappings between gene_id and gene clusters
""" % self.stats)
file.close()
def build_genome_db(args, species):
""" Build FASTA and BT2 database of representative genomes """
import Bio.SeqIO
# fasta database
outfile = open('/'.join([args['outdir'], 'snps/temp/genomes.fa']), 'w')
db_stats = {'total_length': 0, 'total_seqs': 0, 'species': 0}
for sp in species.values():
db_stats['species'] += 1
infile = utility.iopen(sp.paths['fna'])
for r in Bio.SeqIO.parse(infile, 'fasta'):
outfile.write('>%s\n%s\n' % (r.id, str(r.seq).upper()))
db_stats['total_length'] += len(r.seq)
db_stats['total_seqs'] += 1
infile.close()
outfile.close()
# print out database stats
print(" total genomes: %s" % db_stats['species'])
print(" total contigs: %s" % db_stats['total_seqs'])
print(" total base-pairs: %s" % db_stats['total_length'])
# bowtie2 database
inpath = '/'.join([args['outdir'], 'snps/temp/genomes.fa'])
outpath = '/'.join([args['outdir'], 'snps/temp/genomes'])
command = ' '.join([args['bowtie2-build'], inpath, outpath])
args['log'].write('command: ' + command + '\n')
process = subprocess.Popen(command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
def parse_mapping_file(args):
infile = utility.iopen(args['mapfile'])
fields = next(infile).rstrip('\n').split('\t')
for field in ['genome_id', 'species_id']:
if field not in fields:
sys.exit("Error: mapping file '%s' has no field labeled '%s'" %
(args['mapfile'], field))
for field in fields:
if field not in ['genome_id', 'species_id', 'rep_genome']:
sys.exit(
"Error: mapping file '%s' has unknown field labeled '%s'" %
(args['mapfile'], field))
for line in infile:
if len(line.rstrip()) == 0: continue
values = line.rstrip('\n').split('\t')
record = dict([(f, v) for f, v in zip(fields, values)])
if len(values) < len(fields):
sys.exit(
"Error: mapping file '%s' has different number of fields per row"
% args['mapfile'])
if 'rep_genome' in fields and record['rep_genome'] not in ['0', '1']:
sys.exit(
"Error: mapping file '%s' has unknown value '%s' for field 'rep_genome'"
% (args['mapfile'], record['rep_genome']))
yield record
def parse_fasta(self, p_in):
""" Return lookup of seq_id to sequence for PATRIC genes """
seqs = {}
infile = utility.iopen(p_in)
for r in Bio.SeqIO.parse(infile, "fasta"):
seqs[r.id] = str(r.seq).upper()
infile.close()
return seqs
def fetch_centroid(args, species_id):
""" Get the genome_id corresponding to cluster centroid """
inpath = '/'.join(
[args['db'], 'genome_clusters', species_id, 'genomes.txt.gz'])
infile = utility.iopen(inpath)
for line in infile:
if line.split()[2] == 'Y':
return line.split()[1]
def write_genome_info(args, species):
outfile = utility.iopen('%s/genome_info.txt' % args['outdir'], 'w')
header = ['genome_id', 'species_id', 'rep_genome']
outfile.write('\t'.join(header) + '\n')
for sp in species:
for genome_id in sp.genomes:
rep_genome = '1' if genome_id == sp.rep_genome else '0'
values = [genome_id, sp.id, rep_genome]
outfile.write('\t'.join(values) + '\n')
def read_genome(db, species_id):
""" Read in representative genome from reference database """
inpath = '%s/rep_genomes/%s/genome.fna.gz' % (db, species_id)
infile = utility.iopen(inpath)
genome = {}
for r in Bio.SeqIO.parse(infile, 'fasta'):
genome[r.id] = r.seq.upper()
infile.close()
return genome
def read_run_midas_snps(species_id, samples):
""" Open SNP files for species across samples """
infiles = []
for sample in samples:
path = '%s/snps/output/%s.snps.gz' % (sample.dir, species_id)
file = utility.iopen(path)
next(file)
infiles.append(file)
return infiles
def write_genes(self, resume):
""" Concatenate all genes from pangenome into sequence file """
ffn_path = '%s/genes.ffn' % self.dir
if os.path.exists(
ffn_path) and os.stat(ffn_path).st_size > 0 and resume:
return
file = utility.iopen('%s/genes.ffn' % self.dir, 'w')
for gene in self.genes.values():
file.write('>%s\n%s\n' % (gene.id, gene.seq))
file.close()
def parse_tsv(inpath):
""" yield records from tab-delimited file with row and column names """
infile = utility.iopen(inpath)
header = next(infile).rstrip('\n').split('\t')
for line in infile:
split_line = line.rstrip('\n').split('\t')
id = split_line[0]
values = split_line[1:]
yield id, values
infile.close()
def read_ref_bases(args, species_id):
""" Read in reference genome by position """
import Bio.SeqIO
ref = []
centroid_path = '/'.join(
[args['db'], 'genome_clusters', species_id, 'genome.fna.gz'])
infile = utility.iopen(centroid_path)
for rec in Bio.SeqIO.parse(infile, 'fasta'):
for pos in range(1, len(rec.seq) + 1):
ref.append([rec.id, pos, rec.seq[pos - 1].upper()])
return sorted(ref)
def initialize_contigs(species):
contigs = {}
for sp in species.values():
infile = utility.iopen(sp.paths['fna'])
for rec in Bio.SeqIO.parse(infile, 'fasta'):
contig = Contig(rec.id)
contig.seq = str(rec.seq).upper()
contig.length = len(contig.seq)
contig.species_id = sp.id
contigs[contig.id] = contig
infile.close()
return contigs
def read_gene_map(species_id, args):
""" Map 99% centroids to gene_ids at lower level """
gene_to_family = {}
inpath = '%s/genome_clusters/%s/pangenome.map.gz' % (args['db'],
species_id)
infile = utility.iopen(inpath)
fields = next(infile).rstrip().split()
for line in infile:
values = line.rstrip().split()
map = dict([(f, v) for f, v in zip(fields, values)])
gene_to_family[map['99']] = map[args['cluster_pid']]
return gene_to_family
def initialize_genes(args, species):
""" Initialize Gene objects """
genes = {}
# fetch gene_id, species_id, gene length
for sp in species.values():
path = sp.paths['centroids.ffn']
file = utility.iopen(path)
for seq in Bio.SeqIO.parse(file, 'fasta'):
genes[seq.id] = Gene(seq.id)
genes[seq.id].species_id = sp.id
genes[seq.id].length = len(seq.seq)
sp.pangenome_size += 1
file.close()
# fetch marker_id
path = '%s/marker_genes/phyeco.map' % args['db']
file = utility.iopen(path)
reader = csv.DictReader(file, delimiter='\t')
for r in reader:
if r['gene_id'] in genes:
genes[r['gene_id']].marker_id=r['marker_id']
file.close()
return genes
def read_function_map(ref_db, species_id, ontology):
""" Map gene ids to functions for given ontology """
gene_to_functions = {}
inpath = '%s/genome_clusters/%s/pangenome.functions.gz' % (ref_db,
species_id)
infile = utility.iopen(inpath)
for index, line in enumerate(infile):
gene_id, function_id, ont = line.rstrip().split()
if ont == ontology:
if gene_id not in gene_to_functions:
gene_to_functions[gene_id] = []
gene_to_functions[gene_id].append(function_id)
return gene_to_functions
def parse_uclust(self, inpath):
""" Yield formatted records from UCLUST output file """
# centroids are type == 'S'
# non-centroids are type == 'H'
# clusters are type == 'C'
fields = [
'type', 'cluster_id', 'size', 'pid', 'strand', 'skip1', 'skip2',
'skip3', 'gene_id', 'centroid_id'
]
with utility.iopen(inpath) as infile:
for index, line in enumerate(infile):
values = line.rstrip('\n').split('\t')
record = dict([(f, v) for f, v in zip(fields, values)])
yield record
def write_gene_info(self):
""" Record gene info in gene_info.txt """
file = utility.iopen('%s/gene_info.txt' % self.dir, 'w')
header = [
'gene_id', 'genome_id', 'gene_length', 'centroid_99',
'centroid_95', 'centroid_90', 'centroid_85', 'centroid_80',
'centroid_75'
]
file.write('\t'.join(header) + '\n')
for gene_id in sorted(self.genes.keys()):
g = self.genes[gene_id]
values = [
g.id, g.genome_id, g.length, g.centroid_99, g.centroid_95,
g.centroid_90, g.centroid_85, g.centroid_80, g.centroid_75
]
file.write('\t'.join([str(_) for _ in values]) + '\n')
file.close()
def parse_hmmsearch(self, p_in):
""" Parse HMMER domblout files. Return data-type formatted dictionary """
f_in = utility.iopen(p_in)
for line in f_in:
if line[0] == '#': continue
x = line.rstrip().split()
query = x[0]
target = x[3]
evalue = float(x[12])
qcov = (int(x[20]) - int(x[19]) + 1) / float(x[2])
tcov = (int(x[16]) - int(x[15]) + 1) / float(x[5])
yield {
'query': query,
'target': target,
'evalue': evalue,
'qcov': qcov,
'tcov': tcov,
'qlen': int(x[2]),
'tlen': int(x[5])
}
def build_genome_db(args, genome_clusters):
""" Build FASTA and BT2 database from genome cluster centroids """
# fasta database
genomes_fasta = open('/'.join([args['outdir'], 'snps/temp/genomes.fa']),
'w')
genomes_map = open('/'.join([args['outdir'], 'snps/temp/genomes.map']),
'w')
db_stats = {'total_length': 0, 'total_seqs': 0, 'genome_clusters': 0}
for species_id in genome_clusters:
if args['tax_mask'] and fetch_centroid(args,
species_id) in args['tax_mask']:
continue
db_stats['genome_clusters'] += 1
inpath = '/'.join(
[args['db'], 'genome_clusters', species_id, 'genome.fna.gz'])
infile = utility.iopen(inpath)
for line in infile:
genomes_fasta.write(line)
db_stats['total_length'] += len(line.rstrip())
if line[0] == '>':
sid = line.rstrip().lstrip('>').split()[0]
genomes_map.write(sid + '\t' + species_id + '\n')
db_stats['total_seqs'] += 1
# print out database stats
print(" total genomes: %s" % db_stats['genome_clusters'])
print(" total contigs: %s" % db_stats['total_seqs'])
print(" total base-pairs: %s" % db_stats['total_length'])
# bowtie2 database
inpath = '/'.join([args['outdir'], 'snps/temp/genomes.fa'])
outpath = '/'.join([args['outdir'], 'snps/temp/genomes'])
command = ' '.join([args['bowtie2-build'], inpath, outpath])
args['log'].write('command: ' + command + '\n')
process = subprocess.Popen(command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
utility.check_exit_code(process, command)
def compute_phyeco_cov(args, genome_clusters, ref_to_cov, ref_to_cluster):
""" Count number of bp mapped to each PhyEco marker gene """
from numpy import median
# read in set of phyeco markers for normalization
phyeco_ids = set([])
inpath = '/'.join([args['db'], 'marker_genes/pid_cutoffs.txt'])
if not os.path.isfile(inpath): sys.exit("File not found: %s" % inpath)
for line in open(inpath):
phyeco_id, pid = line.rstrip().split('\t')
phyeco_ids.add(phyeco_id)
# read in map of gene to phyeco marker
ref_to_phyeco = {}
for species_id in genome_clusters:
inpath = '/'.join([args['db'], 'genome_clusters', species_id, 'pangenome.marker_genes.gz'])
infile = utility.iopen(inpath)
next(infile)
for line in infile:
gene_id, phyeco_id = line.rstrip().split()
ref_to_phyeco[gene_id] = phyeco_id
# init phyeco coverage
cluster_to_phyeco_to_cov = {}
for species_id in genome_clusters:
cluster_to_phyeco_to_cov[species_id] = {}
for phyeco_id in phyeco_ids:
cluster_to_phyeco_to_cov[species_id][phyeco_id] = 0.0
# compute phyeco coverages
for ref_id, phyeco_id in ref_to_phyeco.items():
species_id = ref_to_cluster[ref_id]
if phyeco_id in phyeco_ids and ref_id in ref_to_cov:
cluster_to_phyeco_to_cov[species_id][phyeco_id] += ref_to_cov[ref_id]
# compute median phyeco cov
cluster_to_norm = {}
for species_id in cluster_to_phyeco_to_cov:
covs = list(cluster_to_phyeco_to_cov[species_id].values())
cluster_to_norm[species_id] = median(covs)
return cluster_to_norm
def format_pileup(args, species, contigs):
""" Parse mpileups and fill in missing positions """
# open outfiles
for sp in species.values():
sp.out = utility.iopen(
'/'.join([args['outdir'],
'snps/output/%s.snps.gz' % sp.id]), 'w')
header = [
'ref_id', 'ref_pos', 'ref_allele', 'alt_allele', 'ref_freq',
'depth', 'count_atcg'
]
sp.out.write('\t'.join(header) + '\n')
sp.contigs = sorted(
[c.id for c in contigs.values() if c.species_id == sp.id])
sp.i = 0 # contig index
sp.j = 0 # position index
# parse pileup
pileup_path = '%s/snps/temp/genomes.mpileup.gz' % args['outdir']
for p in parse_pileup.main(pileup_path):
# fetch contig info
sp = species[contigs[p.ref_id].species_id]
contig = contigs[sp.contigs[sp.i]]
# contig ids don't match
# indicates that one or more upstream contigs have zero coverage
while p.ref_id != contig.id:
write_missing(sp.out,
ref_id=contig.id,
ref_pos=str(sp.j + 1),
ref_allele=contig.seq[sp.j])
sp.j += 1
if sp.j >= contig.length:
sp.i += 1
sp.j = 0
contig = contigs[sp.contigs[sp.i]]
# positions don't match
# indicates that one or more upstream positions have zero coverage
while p.ref_pos != sp.j + 1:
write_missing(sp.out,
ref_id=contig.id,
ref_pos=str(sp.j + 1),
ref_allele=contig.seq[sp.j])
sp.j += 1
if sp.j >= contig.length:
sp.i += 1
sp.j = 0
contig = contigs[sp.contigs[sp.i]]
# match
# write info from pileup
write_present(sp.out, pileup=p)
sp.j += 1
# end of contig
if sp.j >= contig.length:
sp.i += 1
sp.j = 0
# fill in downstream positions & contigs with zero coverage
for sp in species.values():
# no remaining contigs
if sp.i < len(sp.contigs):
# lefover positions on last contig
# indicates that one or more downstream positions have zero coverage
contig = contigs[sp.contigs[sp.i]]
while sp.j < contig.length:
write_missing(sp.out,
ref_id=contig.id,
ref_pos=str(sp.j + 1),
ref_allele=contig.seq[sp.j])
sp.j += 1
# lefover contigs
# indicates that one or more downstream contigs have zero coverage
sp.i += 1
sp.j = 0
while sp.i < len(sp.contigs):
contig = contigs[sp.contigs[sp.i]]
write_missing(sp.out,
ref_id=contig.id,
ref_pos=str(sp.j + 1),
ref_allele=contig.seq[sp.j])
sp.j += 1
if sp.j >= contig.length:
sp.i += 1
sp.j = 0
# close output files
sp.out.close()