def bed_to_bedgraph_by_strand(in_files, out_bedgraphs):
"extend reads to the full fragment length and create a bedgraph from them"
in_bed, in_chrom_sizes = in_files
cmd = (
"""slopBed -i %s -s -r %s -l 0 -g %s | awk '{if ($6 == "+") print $0}' | """
+ "bedItemOverlapCount %s -chromSize=%s.chrom.sizes stdin > %s"
) % (
in_bed,
cfg.getint("DEFAULT", "fragment_size") - cfg.getint("DEFAULT", "tag_size"),
in_chrom_sizes,
cfg.get("DEFAULT", "genome"),
genome_path(),
out_bedgraph[0],
)
sys_call(cmd)
cmd = (
"""slopBed -i %s -s -r %s -l 0 -g %s | awk '{if ($6 == "-") print $0}' | """
+ "bedItemOverlapCount %s -chromSize=%s.chrom.sizes stdin > %s"
) % (
in_bed,
cfg.getint("DEFAULT", "fragment_size") - cfg.getint("DEFAULT", "tag_size"),
in_chrom_sizes,
cfg.get("DEFAULT", "genome"),
genome_path(),
out_bedgraph[1],
)
sys_call(cmd)
def quest_to_wig(in_reads, out_glob, out_template, in_dir, chrom_sizes):
in_template = in_dir + '/tracks/wig_profiles/%s.profile.wig.gz'
for f in ['background_unnormalized', 'background_normalized', 'ChIP_normalized', 'ChIP_unnormalized']:
in_file = in_template % f
out_file = out_template % f
#shutil.copy(in_file, out_file)
sys_call('gunzip -c -d %s > %s' % (in_file, out_file))
def merge_comparison_types(in_files, out_merged):
"""concatenate the comparison types together for plotting"""
cmd = 'cat %s > %s ' % (in_files[0], out_merged)
sys_call(cmd, file_log=False)
# skip the header for remaining files
for f in in_files[1:]:
cmd = 'sed 1d %s >> %s' % (f, out_merged)
sys_call(cmd, file_log=False)
def remove_nonoverlapping_reads(in_bed, out_bed, min_read_count):
"""
Remove mapped reads that don't overlap with at least *min_read_count* reads
"""
cmd = "intersectBed -wa -c -a %s -b %s | awk '$(NF) >= %s' |" \
r"cut -f 1,2,3,4,5,6 > %s" % (in_bed, in_bed, min_read_count + 1,
out_bed)
sys_call(cmd, file_log=False)
def run_quest(in_reads, out_peaks, chrom_sizes):
"""Run QuEST on the given treatment and control data"""
in_treat = filter(lambda f: '.treat.' in f, in_reads)[0]
in_control = filter(lambda f: '.control.' in f, in_reads)[0]
sys_call('echo "y\n1\n2\ny\n" | generate_QuEST_parameters.pl -QuEST_align_ChIP %s '
'-QuEST_align_RX_noIP %s -gt %s -ap %s_output -silent' %
(in_treat, in_control, chrom_sizes, in_treat))
shutil.copy('%s_output/calls/peak_caller.ChIP.out.accepted' % in_treat, out_peaks)
def clip_and_sort_peaks(in_bed, out_sorted):
"""Sort the bed file and constrain bed regions to chromosome sizes"""
with tempfile.NamedTemporaryFile() as tmp_clipped:
cmd = "bedClip %s %s.chrom.sizes %s" % (in_bed, genome_path(), tmp_clipped.name)
sys_call(cmd)
# cmd = 'bedSort %s %s' % (out_clipped, out_sorted)
cmd = r"sort -t $'\t' -k 1,1 -k 2,2n -S 2G %s > %s" % (tmp_clipped.name, out_sorted)
sys_call(cmd)
def discover_nmica_motifs(in_fasta, out_motifs):
"""Discover sequence motifs in peaks by running nestedMICA"""
cmd = 'nminfer -seqs %s %s ' % (in_fasta, cfg.get('motifs', 'nmica_params'))
sys_call(cmd)
motifs_name = in_fasta.replace('.fasta', '.motifs.xms')
sys_call('mv motifs.xms %s' % motifs_name)
motifs = sequence_motif.parse_xms_motifs(motifs_name)
pickle.dump(motifs, open(out_motifs, 'w'))
def discover_meme_motifs(in_fasta, out_motifs):
"""Discover sequence motifs in peaks by running meme"""
cmd = 'meme %s %s -oc %s_meme_out ' % (
in_fasta, cfg.get('motifs', 'meme_params'), out_motifs)
#if 'top' in in_fasta and 'around' in in_fasta:
sys_call(cmd)
motifs = sequence_motif.parseMemeMotifs('%s_meme_out/meme.txt' %
out_motifs)
pickle.dump(motifs, open(out_motifs, 'w'))
def deploy_track_files(in_files, out_header):
"""Copy UCSC tracks to public url"""
remote = cfg.get("visualization", "remote_ssh_dir")
remote_host = remote.split(":")[0]
remote_dir = remote.split(":")[1]
for in_track in in_files:
sys_call("ssh %s mkdir -p %s" % (remote_host, remote_dir))
sys_call("scp %s %s" % (in_track, remote))
touch(out_header)
def discover_meme_motifs(in_fasta, out_motifs):
"""Discover sequence motifs in peaks by running meme"""
cmd = 'meme %s %s -oc %s_meme_out ' % (in_fasta,
cfg.get('motifs', 'meme_params'),
out_motifs)
#if 'top' in in_fasta and 'around' in in_fasta:
sys_call(cmd)
motifs = sequence_motif.parseMemeMotifs('%s_meme_out/meme.txt' % out_motifs)
pickle.dump(motifs, open(out_motifs, 'w'))
def deploy_track_files(in_files, out_header):
"""Copy UCSC tracks to public url"""
remote = cfg.get('visualization', 'remote_ssh_dir')
remote_host = remote.split(':')[0]
remote_dir = remote.split(':')[1]
for in_track in in_files:
sys_call('ssh %s mkdir -p %s' % (remote_host, remote_dir))
sys_call('scp %s %s' % (in_track, remote))
touch(out_header)
def clip_and_sort_peaks(in_bed, out_sorted):
"""Sort the bed file and constrain bed regions to chromosome sizes"""
with tempfile.NamedTemporaryFile() as tmp_clipped:
cmd = 'bedClip %s %s.chrom.sizes %s' % (in_bed, genome_path(),
tmp_clipped.name)
sys_call(cmd)
#cmd = 'bedSort %s %s' % (out_clipped, out_sorted)
cmd = r"sort -t $'\t' -k 1,1 -k 2,2n -S 2G %s > %s" % (tmp_clipped.name, out_sorted)
sys_call(cmd)
def merge_strands(in_files, out_merged):
"""concatenate the strand-specific analyses for plotting"""
# output the first file in its entirety
cmd = 'cat %s > %s ' % (in_files[0], out_merged)
sys_call(cmd, file_log=False)
# skip the header for remaining files
for f in in_files[1:]:
cmd = 'sed 1d %s >> %s' % (f, out_merged)
sys_call(cmd, file_log=False)
def discover_nmica_motifs(in_fasta, out_motifs):
"""Discover sequence motifs in peaks by running nestedMICA"""
cmd = 'nminfer -seqs %s %s ' % (in_fasta, cfg.get('motifs',
'nmica_params'))
sys_call(cmd)
motifs_name = in_fasta.replace('.fasta', '.motifs.xms')
sys_call('mv motifs.xms %s' % motifs_name)
motifs = sequence_motif.parse_xms_motifs(motifs_name)
pickle.dump(motifs, open(out_motifs, 'w'))
def run_mosaik_align(in_files, out_align):
'align reads to reference using MosaikAligner'
# MosaikAligner -in sequence_archives/c_elegans_chr2_test.dat -out sequence_archives/c_elegans_chr2_test_aligned.dat -ia reference/c.elegans_chr2.dat -hs 14 -act 17 -mm 2 -m unique
in_reads, in_genome_dat, in_genome_jump, _, _ = in_files
in_genome_jump = in_genome_jump.replace('_keys.jmp', '')
cmd = 'MosaikAligner -in %s -ia %s -j %s -out %s -hs %s %s'
cmd = cmd % (in_reads, in_genome_dat, in_genome_jump, out_align,
cfg.getint('mapping', 'mosaik_hash_size'),
cfg.get('mapping', 'mosaik_params'))
sys_call(cmd)
def run_mosaik_align(in_files, out_align):
'align reads to reference using MosaikAligner'
# MosaikAligner -in sequence_archives/c_elegans_chr2_test.dat -out sequence_archives/c_elegans_chr2_test_aligned.dat -ia reference/c.elegans_chr2.dat -hs 14 -act 17 -mm 2 -m unique
in_reads, in_genome_dat, in_genome_jump, _, _ = in_files
in_genome_jump = in_genome_jump.replace('_keys.jmp', '')
cmd = 'MosaikAligner -in %s -ia %s -j %s -out %s -hs %s %s'
cmd = cmd % (in_reads, in_genome_dat, in_genome_jump, out_align,
cfg.getint('mapping', 'mosaik_hash_size'),
cfg.get('mapping', 'mosaik_params'))
sys_call(cmd)
def bed_to_bedgraph(in_files, out_bedgraph):
'extend reads to the full fragment length and create a bedgraph from them'
in_bed, in_chrom_sizes = in_files
cmd = ('slopBed -i %s -s -r %s -l 0 -g %s | ' + \
'bedItemOverlapCount %s -chromSize=%s.chrom.sizes stdin > %s') % (
in_bed,
cfg.getint('DEFAULT','fragment_size') - \
cfg.getint('DEFAULT','tag_size'),
in_chrom_sizes, cfg.get('DEFAULT', 'genome'),
genome_path(), out_bedgraph)
sys_call(cmd)
def get_microRNA(_, out_mirna):
"""retrieve microRNA genes from UCSC"""
url = 'http://hgdownload.cse.ucsc.edu/goldenPath/%s/database/wgRna.txt.gz'
url = url % cfg.get('DEFAULT', 'genome')
sys_call('wget -N -P . %s' % url)
sys_call('gunzip -f wgRna.txt.gz')
with open(out_mirna, 'w') as outfile:
for line in open('wgRna.txt'):
(bin, chrom, start, end, name, score,
strand, thickStart, thickEnd, type) = line.strip().split('\t')
outfile.write('\t'.join([chrom, start, end, name + '_' + type, score, strand]) + '\n')
def get_ssaha2_hashtable(in_genome, out_ssaha2):
"""Use ssaha2Build to generate a hash table for the genetic
sequences stored in an input .fasta file
ssaha2Build writes five files to disk, each preceded by
the hash name. Their file extensions are:
.base, .body, .head, .name, .size
"""
#TODO: add useful parameters to cmd and config file
cmd = 'ssaha2Build -save %s %s' % (out_ssaha2, in_genome)
sys_call(cmd)
def run_glitr(in_files, out_peaks):
"""Call peaks with GLITR"""
in_treat = filter(lambda f: '.treat.' in f, in_files)[0]
in_control = filter(lambda f: '.control.' in f, in_files)[0]
glitr_dir = in_treat + '.GLITR_out'
cmd = ('rm -r %s; mkdir %s; cd %s; GLITR.pl --CHIP=../%s ' + \
'--CONTROL=../%s --GENOME=%s %s ') % (
glitr_dir, glitr_dir, glitr_dir, in_treat, in_control,
cfg.get('DEFAULT', 'genome').upper(),
cfg.get('peaks', 'glitr_params'))
sys_call(cmd)
sys_call('cp %s/allChIP.FDR_*PercentFDR %s' % (glitr_dir, out_peaks))
def get_microRNA(_, out_mirna):
"""retrieve microRNA genes from UCSC"""
url = 'http://hgdownload.cse.ucsc.edu/goldenPath/%s/database/wgRna.txt.gz'
url = url % cfg.get('DEFAULT', 'genome')
sys_call('wget -N -P . %s' % url)
sys_call('gunzip -f wgRna.txt.gz')
with open(out_mirna, 'w') as outfile:
for line in open('wgRna.txt'):
(bin, chrom, start, end, name, score, strand, thickStart, thickEnd,
type) = line.strip().split('\t')
outfile.write('\t'.join(
[chrom, start, end, name + '_' + type, score, strand]) + '\n')
def bed_to_bedgraph(in_files, out_bedgraph):
"extend reads to the full fragment length and create a bedgraph from them"
in_bed, in_chrom_sizes = in_files
cmd = ("slopBed -i %s -s -r %s -l 0 -g %s | " + "bedItemOverlapCount %s -chromSize=%s.chrom.sizes stdin > %s") % (
in_bed,
cfg.getint("DEFAULT", "fragment_size") - cfg.getint("DEFAULT", "tag_size"),
in_chrom_sizes,
cfg.get("DEFAULT", "genome"),
genome_path(),
out_bedgraph,
)
sys_call(cmd)
def get_ssaha2_hashtable(in_genome, out_ssaha2):
"""Use ssaha2Build to generate a hash table for the genetic
sequences stored in an input .fasta file
ssaha2Build writes five files to disk, each preceded by
the hash name. Their file extensions are:
.base, .body, .head, .name, .size
"""
#TODO: add useful parameters to cmd and config file
cmd = 'ssaha2Build -save %s %s' % (out_ssaha2, in_genome)
sys_call(cmd)
def run_ssaha2(in_fastq, out_ssaha2):
""" Runs ssaha2 command using the prebuilt hash table from
get_ssaha2_hashtable.
The ssaha2 command maps DNA sequence reads onto a genomic
reference sequence using a combination of word hashing and
dynamic programming. (From ssaha2 manual)
"""
#TODO: add useful parameters to cmd and config file
#cmd = 'ssaha2 -outfile %s -save %s %s' % (out_ssaha2, hash_name, in_fastq)
cmd = 'ssaha2 -outfile %s -disk 1 -save %s %s'
cmd = cmd % (out_ssaha2, (cfg.get('mapping', 'ssaha2_hash_name')), in_fastq)
sys_call(cmd)
def run_ssaha2(in_fastq, out_ssaha2):
""" Runs ssaha2 command using the prebuilt hash table from
get_ssaha2_hashtable.
The ssaha2 command maps DNA sequence reads onto a genomic
reference sequence using a combination of word hashing and
dynamic programming. (From ssaha2 manual)
"""
#TODO: add useful parameters to cmd and config file
#cmd = 'ssaha2 -outfile %s -save %s %s' % (out_ssaha2, hash_name, in_fastq)
cmd = 'ssaha2 -outfile %s -disk 1 -save %s %s'
cmd = cmd % (out_ssaha2, (cfg.get('mapping', 'ssaha2_hash_name')), in_fastq)
sys_call(cmd)
def run_macs(in_files, out_peaks, max_fdr):
"""Call peak with MACS (v1.3).
Apply a maximum FDR threshold and treat centers as peak summits
"""
in_treat, in_control = in_files[0]
matches = re.search(r'(.*\.treat)(.*)\.mapped_reads', in_treat).groups()
name = matches[0] + matches[1] + '.macs.peaks'
max_fdr = cfg.getfloat('peaks', 'max_FDR')
cmd = 'macs -t %s -c %s --name=%s %s' % (in_treat, in_control, name,
cfg.get('peaks', 'macs_params'))
sys_call(cmd)
# convert to proper bedfile- ints for score and + for strand
with open(out_peaks, 'w') as outfile:
with open(name + '_peaks.xls') as infile:
for index, line in enumerate(itertools.ifilter(
bedCommentFilter, infile)):
fields = line.split('\t')
if fields[0] == 'chr':
continue # skip header
start = str(max(0, int(fields[1])))
score = str(max(0, min(1000, int(float(fields[6])))))
fdr = float(fields[8])
if fdr <= max_fdr:
outfile.write('\t'.join([fields[0], start, fields[2],
'MACS_peak_%s' % (index + 1), score]) +
'\t+\n')
# take region surrounding the peak center as the summit
summit_size = cfg.getint('peaks', 'peak_summit_size')
with open(out_peaks + '_summits.%s_around' % \
cfg.get('peaks', 'peak_summit_size'), 'w') as outfile:
with open(name + '_peaks.xls') as infile:
for index, line in enumerate(itertools.ifilter(bedCommentFilter,
infile)):
fields = line.strip().split('\t')
if fields[0] == 'chr':
continue # skip header
score = str(max(0, min(1000, int(float(fields[6])))))
p_start, p_stop = max(0, int(fields[1])), int(fields[2])
p_center = p_start + (p_stop - p_start) / 2
s_start = p_center - summit_size / 2
s_stop = p_center + summit_size / 2
fdr = float(fields[8])
if fdr <= max_fdr:
outfile.write('\t'.join([fields[0], str(s_start),
str(s_stop),
'MACS_peak_%s' % (index + 1), score])
+ '\t+\n')
def get_nearest_features(in_files, _, out_pattern):
"""Calculate the distance from each peak to the nearest features"""
print in_files
print out_pattern
in_peaks, chrom_sizes, all_features = in_files[0], in_files[1], in_files[
2:]
if len(all_features) == 0:
raise RuntimeError("No features present to compare to!")
# get distances for each feature
tmp_output = tempfile.NamedTemporaryFile(delete=False)
for in_feature in all_features:
distances = []
all_distances = []
cmd = 'closestBed -a %s -b %s -t first -D ref > %s' % (
in_peaks, in_feature, tmp_output.name)
sys_call(cmd, file_log=False)
with open(tmp_output.name) as infile:
for line in infile:
if not line:
continue
fields = line.strip().split('\t')
dist = int(fields[-1])
#if int(fields[1]) < int(fields[7]):
# dist *= -1
distances.append(dist)
all_distances.append(distances)
cmd = 'shuffleBed -chrom -i %s -g %s | closestBed -a stdin -b %s -t first -D ref > %s' % (
in_peaks, chrom_sizes, in_feature, tmp_output.name)
sys_call(cmd, file_log=False)
distances = []
with open(tmp_output.name) as infile:
for line in infile:
if not line:
continue
fields = line.strip().split('\t')
dist = int(fields[-1])
#if int(fields[1]) < int(fields[7]):
# dist *= -1
distances.append(dist)
all_distances.append(distances)
with open(out_pattern % in_feature, 'w') as outfile:
outfile.write('\t'.join([in_feature, 'Random']) + '\n') # header
for d in zip(*all_distances):
outfile.write('\t'.join(map(str, d)) +
'\n') # distance as column
os.unlink(tmp_output.name)
def find_nearby_genes(in_files, out_genes):
"""report which genes are within a certain distance of a peak"""
in_peaks, in_genes = in_files[0]
tmp_output = tempfile.NamedTemporaryFile(delete=False).name
cmd = 'closestBed -a %s -b %s -t first -d > %s' % (in_peaks, in_genes,
tmp_output)
sys_call(cmd)
with open(tmp_output) as infile:
with open(out_genes, 'w') as outfile:
for line in infile:
if not line:
continue
fields = line.strip().split('\t')
dist = int(fields[-1])
if abs(dist) <= cfg.getint('genes', 'nearby_genes_max_dist'):
outfile.write(line)
os.unlink(tmp_output)
def find_nearby_genes(in_files, out_genes):
"""report which genes are within a certain distance of a peak"""
in_peaks, in_genes = in_files[0]
tmp_output = tempfile.NamedTemporaryFile(delete=False).name
cmd = 'closestBed -a %s -b %s -t first -d > %s' % (in_peaks,
in_genes, tmp_output)
sys_call(cmd)
with open(tmp_output) as infile:
with open(out_genes, 'w') as outfile:
for line in infile:
if not line:
continue
fields = line.strip().split('\t')
dist = int(fields[-1])
if abs(dist) <= cfg.getint('genes', 'nearby_genes_max_dist'):
outfile.write(line)
os.unlink(tmp_output)
def get_nearest_features(in_files, _, out_pattern):
"""Calculate the distance from each peak to the nearest features"""
print in_files
print out_pattern
in_peaks, chrom_sizes, all_features = in_files[0], in_files[1], in_files[2:]
if len(all_features) == 0:
raise RuntimeError("No features present to compare to!")
# get distances for each feature
tmp_output = tempfile.NamedTemporaryFile(delete=False)
for in_feature in all_features:
distances = []
all_distances = []
cmd = 'closestBed -a %s -b %s -t first -D ref > %s' % (in_peaks, in_feature,
tmp_output.name)
sys_call(cmd, file_log=False)
with open(tmp_output.name) as infile:
for line in infile:
if not line:
continue
fields = line.strip().split('\t')
dist = int(fields[-1])
#if int(fields[1]) < int(fields[7]):
# dist *= -1
distances.append(dist)
all_distances.append(distances)
cmd = 'shuffleBed -chrom -i %s -g %s | closestBed -a stdin -b %s -t first -D ref > %s' % (
in_peaks, chrom_sizes, in_feature, tmp_output.name)
sys_call(cmd, file_log=False)
distances = []
with open(tmp_output.name) as infile:
for line in infile:
if not line:
continue
fields = line.strip().split('\t')
dist = int(fields[-1])
#if int(fields[1]) < int(fields[7]):
# dist *= -1
distances.append(dist)
all_distances.append(distances)
with open(out_pattern % in_feature, 'w') as outfile:
outfile.write('\t'.join([in_feature, 'Random']) + '\n') # header
for d in zip(*all_distances):
outfile.write('\t'.join(map(str, d)) + '\n') # distance as column
os.unlink(tmp_output.name)
def run_macs14(in_files, out_peaks, max_fdr):
"""Call peaks using MACS (v1.4). Apply a maximum FDR threshold."""
in_treat, in_control = in_files[0]
matches = re.search(r'(.*\.treat)(.*)\.mapped_reads', in_treat).groups()
name = matches[0] + matches[1] + '.macs14.peaks'
cmd = 'macs14 -t %s -c %s --name=%s %s --diag' % (in_treat, in_control, name,
cfg.get('peaks', 'macs14_params'))
sys_call(cmd)
peaks_to_keep = set()
# convert to proper bedfile- ints for score and + for strand
with open(out_peaks, 'w') as outfile:
with open(name + '_peaks.xls') as infile:
for index, line in enumerate(itertools.ifilter(bedCommentFilter,
infile)):
fields = line.split('\t')
if fields[0] == 'chr':
continue # skip header
start = str(max(0, int(fields[1])))
score = str(max(0, min(1000, int(float(fields[6])))))
fdr = float(fields[8])
if fdr <= max_fdr:
outfile.write('\t'.join([fields[0], start, fields[2],
'MACS14_peak_%s' % (index + 1), score])
+ '\t+\n')
peaks_to_keep.add(index)
# take region surrounding the peak summit
summit_size = cfg.getint('peaks', 'peak_summit_size')
with open(out_peaks + '_summits.%s_around' % \
cfg.get('peaks', 'peak_summit_size'), 'w') as outfile:
with open(name + '_summits.bed') as infile:
for index, line in enumerate(itertools.ifilter(bedCommentFilter,
infile)):
fields = line.strip().split('\t')
if fields[0] == 'chr':
continue # skip header
# score is number of reads at summit
score = str(max(0, min(1000, int(float(fields[-1])))))
start = str(max(0, int(fields[1]) - summit_size / 2))
stop = str(int(fields[2]) + summit_size / 2)
if index in peaks_to_keep:
outfile.write('\t'.join([fields[0], start, stop,
'MACS_peak_%s' % (index + 1), score])
+ '\t+\n')
def bed_to_bedgraph_by_strand(in_files, out_bedgraphs):
'extend reads to the full fragment length and create a bedgraph from them'
in_bed, in_chrom_sizes = in_files
cmd = ("""slopBed -i %s -s -r %s -l 0 -g %s | awk '{if ($6 == "+") print $0}' | """ + \
'bedItemOverlapCount %s -chromSize=%s.chrom.sizes stdin > %s') % (
in_bed,
cfg.getint('DEFAULT','fragment_size') - \
cfg.getint('DEFAULT','tag_size'),
in_chrom_sizes, cfg.get('DEFAULT', 'genome'),
genome_path(), out_bedgraph[0])
sys_call(cmd)
cmd = ("""slopBed -i %s -s -r %s -l 0 -g %s | awk '{if ($6 == "-") print $0}' | """ + \
'bedItemOverlapCount %s -chromSize=%s.chrom.sizes stdin > %s') % (
in_bed,
cfg.getint('DEFAULT','fragment_size') - \
cfg.getint('DEFAULT','tag_size'),
in_chrom_sizes, cfg.get('DEFAULT', 'genome'),
genome_path(), out_bedgraph[1])
sys_call(cmd)
def get_refseq_genes(_, out_genes):
"""Download refseq genes from UCSC and reformat as BED"""
url = 'http://hgdownload.cse.ucsc.edu/goldenPath/%s/database/refGene.txt.gz'
url = url % cfg.get('DEFAULT', 'genome')
sys_call('wget -N -P . %s' % url)
sys_call('gunzip -f refGene.txt.gz')
sys_call('mv refGene.txt %s' % out_genes)
def get_refseq_genes(_, out_genes):
"""Download refseq genes from UCSC and reformat as BED"""
url = 'http://hgdownload.cse.ucsc.edu/goldenPath/%s/database/refGene.txt.gz'
url = url % cfg.get('DEFAULT', 'genome')
sys_call('wget -N -P . %s' % url)
sys_call('gunzip -f refGene.txt.gz')
sys_call('mv refGene.txt %s' % out_genes)
def run_macs14_no_control(in_treat, out_peaks):
"""Call peaks using MACS (v1.4) without control data"""
cmd = 'macs14 -t %s --name=%s %s' % (in_treat, out_peaks,
cfg.get('peaks', 'macs14_params'))
sys_call(cmd)
peaks_to_keep = set()
# convert to proper bedfile- ints for score and + for strand
with open(out_peaks, 'w') as outfile:
with open(out_peaks + '_peaks.xls') as infile:
for index, line in enumerate(itertools.ifilter(bedCommentFilter,
infile)):
fields = line.split('\t')
if fields[0] == 'chr':
continue # skip header
start = str(max(0, int(fields[1])))
score = str(max(0, min(1000, int(float(fields[6])))))
outfile.write('\t'.join([fields[0], start, fields[2],
'MACS14_peak_%s' % (index + 1), score])
+ '\t+\n')
peaks_to_keep.add(index)
# take region surrounding the peak summit
summit_size = cfg.getint('peaks', 'peak_summit_size')
with open(out_peaks + '_summits.%s_around' % \
cfg.get('peaks', 'peak_summit_size'), 'w') as outfile:
with open(out_peaks + '_summits.bed') as infile:
for index, line in enumerate(itertools.ifilter(bedCommentFilter,
infile)):
fields = line.strip().split('\t')
if fields[0] == 'chr':
continue # skip header
# score is number of reads at summit
score = str(max(0, min(1000, int(float(fields[-1])))))
start = str(max(0, int(fields[1]) - summit_size / 2))
stop = str(int(fields[2]) + summit_size / 2)
if index in peaks_to_keep:
outfile.write('\t'.join([fields[0], start, stop,
'MACS_peak_%s' % (index + 1), score])
+ '\t+\n')
def maq_map_reads(in_files, out_map):
""" Use maq match to align the reads to the reference.
Input files are in binary format and output is in .map format.
"""
cmd = 'maq match %s %s %s' % (out_map, in_files[0], in_files[1])
sys_call(cmd)
def get_polyA_DB(_, out_db, genome_build):
cmd = r"curl 'http://hgdownload.cse.ucsc.edu/goldenPath/%s/database/polyaDb.txt.gz' | gunzip - | cut -d $'\t' -f 2- > %s"
cmd = cmd % (genome_build, out_db)
sys_call(cmd, file_log=False)
def wig_to_bigwig(in_wig, out_bigwig):
"""Convert the wig file to a bigwig file"""
cmd = 'wigToBigWig %s %s.chrom.sizes %s' % (in_wig, genome_path(), out_bigwig)
sys_call(cmd)
def bedgraph_to_bigwig(in_bedgraph, out_bigwig):
"""Convert the bedgraph file to .bigwig for viewing on UCSC"""
cmd = 'bedGraphToBigWig %s %s.chrom.sizes %s' % (in_bedgraph, genome_path(),
out_bigwig)
sys_call(cmd)
def wig_to_bigwig(in_wig, out_bigwig):
"""Convert the wig file to a bigwig file"""
cmd = "wigToBigWig %s %s.chrom.sizes %s" % (in_wig, genome_path(), out_bigwig)
sys_call(cmd)
def remove_terminal_exon(in_files, out_bed):
"""Remove all exons but the last one using intersectBed"""
in_bed, exon_file = in_files
cmd = 'intersectBed -v -a %s -b %s > %s' % (in_bed, exon_file, out_bed)
sys_call(cmd, file_log=False)
def convert_gff3_genes_to_bed(in_gff3, out_gene_pred):
"""convert gff3 genes to UCSC's genePred format"""
sys_call('gff3ToGenePred %s %s' % (in_gff3, out_gene_pred), file_log=False)
def maq_index_reads(in_fastq, out_bfq):
""" Use maq fastq2bfq to convert read sequences in .fastq
format to BFQ format, which is a binary representation.
"""
cmd = 'maq fastq2bfq %s %s' % (in_fastq, out_bfq)
sys_call(cmd)
def bedgraph_to_bigwig(in_bedgraph, out_bigwig):
"""Convert the bedgraph file to .bigwig for viewing on UCSC"""
cmd = "bedGraphToBigWig %s %s.chrom.sizes %s" % (in_bedgraph, genome_path(), out_bigwig)
sys_call(cmd)
def uniquefy_downsample_reads(in_files, out_files):
"""Uniquefy sequence reads then downsample so the total unique tag count in
treatment and control is the same. This may generate many downsampled datasets.
"""
# WARNING: this is a circular dependency. It has to be included at runtime
# Top-level import will cause this module to load only 1/2 way
# we import here because we need to call this function directly,
# and not just when using ruffus
from hts_waterworks.visualize import bed_uniquefy
if not cfg.getboolean('peaks', 'downsample_reads'):
with log_mtx:
log.debug('NOT downsampling the sequence reads!')
else:
in_treat, in_control = in_files
out_treat_template = re.sub(r'mapped_reads$',
'matched_size_%s.mapped_reads', in_treat)
out_control_template = re.sub(r'mapped_reads$',
'matched_size_%s.mapped_reads', in_control)
if out_treat_template == in_treat:
raise RuntimeError('regex substitution failed from %s to %s' % (
in_treat, out_treat_template))
if out_control_template == in_control:
raise RuntimeError('regex substitution failed from %s to %s' % (
in_control, out_control_template))
tmp_t_sorted = tempfile.NamedTemporaryFile(delete=False).name
tmp_c_sorted = tempfile.NamedTemporaryFile(delete=False).name
tmp_t_unique = tempfile.NamedTemporaryFile(delete=False).name
tmp_c_unique = tempfile.NamedTemporaryFile(delete=False).name
# sort the reads
bed_clip_and_sort(in_treat, tmp_t_sorted)
bed_clip_and_sort(in_control, tmp_c_sorted)
# uniquefy the reads
bed_uniquefy(tmp_t_sorted, tmp_t_unique,
cfg.getint('visualization', 'uniquefy_track_max_reads'))
bed_uniquefy(tmp_c_sorted, tmp_c_unique,
cfg.getint('visualization', 'uniquefy_track_max_reads'))
total_treat = sum(1 for l in open(tmp_t_unique))
total_control = sum(1 for l in open(tmp_c_unique))
if total_treat == total_control:
with log_mtx:
log.debug('No downsampling required-- tag counts identical')
else:
# downsample num_down_sample times
for i in xrange(cfg.getint('peaks', 'num_down_samples')):
out_treat = out_treat_template % i
out_control = out_control_template % i
if total_treat > total_control:
# reduce number of treatment reads
inds_to_keep = set(random.sample(xrange(total_treat),
total_control))
in_orig, out_orig = tmp_c_unique, out_control
in_subset, out_subset = tmp_t_unique, out_treat
else:
# reduce number of control reads
inds_to_keep = set(random.sample(xrange(total_control),
total_treat))
in_orig, out_orig = tmp_t_unique, out_treat
in_subset, out_subset = tmp_c_unique, out_control
sys_call('cp %s %s' % (in_orig, out_orig))
# subset the tags
with open(in_subset) as infile:
with open(out_subset, 'w') as outfile:
outfile.writelines(line for i, line in enumerate(infile)
if i in inds_to_keep)
for f in [tmp_t_sorted, tmp_t_unique, tmp_c_sorted, tmp_c_unique]:
os.unlink(f)
def maq_view_reads(in_map, out_map):
""" Use maq mapview to generate a human readable .map
format.
"""
cmd = 'maq mapview %s > %s' % (in_map, out_map)
sys_call(cmd)
def bed_to_bigbed(in_bed, out_bigbed):
"""Convert a BED file to .bigbed for viewing on UCSC browser"""
cmd = "bedToBigBed %s %s.chrom.sizes %s" % (in_bed, genome_path(), out_bigbed)
sys_call(cmd)
def uniquefy_downsample_reads(in_files, out_files):
"""Uniquefy sequence reads then downsample so the total unique tag count in
treatment and control is the same. This may generate many downsampled datasets.
"""
# WARNING: this is a circular dependency. It has to be included at runtime
# Top-level import will cause this module to load only 1/2 way
# we import here because we need to call this function directly,
# and not just when using ruffus
from hts_waterworks.visualize import bed_uniquefy
if not cfg.getboolean('peaks', 'downsample_reads'):
with log_mtx:
log.debug('NOT downsampling the sequence reads!')
else:
in_treat, in_control = in_files
out_treat_template = re.sub(r'mapped_reads$',
'matched_size_%s.mapped_reads', in_treat)
out_control_template = re.sub(r'mapped_reads$',
'matched_size_%s.mapped_reads', in_control)
if out_treat_template == in_treat:
raise RuntimeError('regex substitution failed from %s to %s' % (
in_treat, out_treat_template))
if out_control_template == in_control:
raise RuntimeError('regex substitution failed from %s to %s' % (
in_control, out_control_template))
tmp_t_sorted = tempfile.NamedTemporaryFile(delete=False).name
tmp_c_sorted = tempfile.NamedTemporaryFile(delete=False).name
tmp_t_unique = tempfile.NamedTemporaryFile(delete=False).name
tmp_c_unique = tempfile.NamedTemporaryFile(delete=False).name
# sort the reads
bed_clip_and_sort(in_treat, tmp_t_sorted)
bed_clip_and_sort(in_control, tmp_c_sorted)
# uniquefy the reads
bed_uniquefy(tmp_t_sorted, tmp_t_unique,
cfg.getint('visualization', 'uniquefy_track_max_reads'))
bed_uniquefy(tmp_c_sorted, tmp_c_unique,
cfg.getint('visualization', 'uniquefy_track_max_reads'))
total_treat = sum(1 for l in open(tmp_t_unique))
total_control = sum(1 for l in open(tmp_c_unique))
if total_treat == total_control:
with log_mtx:
log.debug('No downsampling required-- tag counts identical')
else:
# downsample num_down_sample times
for i in xrange(cfg.getint('peaks', 'num_down_samples')):
out_treat = out_treat_template % i
out_control = out_control_template % i
if total_treat > total_control:
# reduce number of treatment reads
inds_to_keep = set(random.sample(xrange(total_treat),
total_control))
in_orig, out_orig = tmp_c_unique, out_control
in_subset, out_subset = tmp_t_unique, out_treat
else:
# reduce number of control reads
inds_to_keep = set(random.sample(xrange(total_control),
total_treat))
in_orig, out_orig = tmp_t_unique, out_treat
in_subset, out_subset = tmp_c_unique, out_control
sys_call('cp %s %s' % (in_orig, out_orig))
# subset the tags
with open(in_subset) as infile:
with open(out_subset, 'w') as outfile:
outfile.writelines(line for i, line in enumerate(infile)
if i in inds_to_keep)
for f in [tmp_t_sorted, tmp_t_unique, tmp_c_sorted, tmp_c_unique]:
os.unlink(f)
def bed_to_bigbed(in_bed, out_bigbed):
"""Convert a BED file to .bigbed for viewing on UCSC browser"""
cmd = 'bedToBigBed %s %s.chrom.sizes %s' % (in_bed,
genome_path(), out_bigbed)
sys_call(cmd)
def maq_index_reference(in_fasta, out_bfa):
""" Use maq fasta2bfa to convert reference sequences in .fasta
format to BFA format, which is a binary representation.
"""
cmd = 'maq fasta2bfa %s %s' % (in_fasta, out_bfa)
sys_call(cmd)
def merge_adjacent_reads(in_bed, out_pattern, window_width, iterations,
out_merged, out_pileup, min_read_count):
"""Reassign read ends to a weighted average of adjacent reads"""
# helper functions for parsing bed files
filter_lines = lambda l: l.strip() and (not l.startswith('#') or \
l.startswith('"'))
read_bed_lines = lambda infile: itertools.ifilter(filter_lines, infile)
# sort the input by chrom, stop
tmpfile = in_bed + '.merged_adjacent_sorted'
cmd = r"sort -t $'\t' -k 1,1 -k 3g,3 %s > %s" % (in_bed, tmpfile)
print cmd
sys_call(cmd, file_log=False)
p_file = tmpfile
outfile_pileup = None # used on last iteration to generate the final pileup
for i in range(iterations):
print 'merge iteration %s' % i
# read in from output of previous iteration
infile = read_bed_lines(open(p_file))
# output to a temp file except on the last iteration
if i != iterations - 1:
p_file = in_bed + '.merge_adjacent_%s' % i
else:
p_file = out_merged
outfile_pileup = open(out_pileup, 'w')
outfile = open(p_file, 'w')
# parse first line
(chrom, start, stop, name,
score, strand) = infile.next().strip().split('\t')[:6]
if strand == '+':
p_chrom, p_stops, p_names, p_strands = (chrom, [int(stop)],
[name], [strand])
else:
p_chrom, p_stops, p_names, p_strands = (chrom, [int(start)],
[name], [strand])
print 'first line:', chrom, start, stop, name, score, strand
for index, line in enumerate(infile):
try:
(chrom, start, stop,
name, score, strand) = line.strip().split('\t')[:6]
except:
print index, 'this line:', line
raise
if strand == '+':
stop = int(stop)
else:
stop = int(start) + 1
# is next read too far from first recorded?
if p_chrom != chrom or (len(p_stops) > 0 and
abs(p_stops[0] - stop) > window_width):
if len(p_stops) == 0 or len(p_names) == 0:
print 'error!'
print line
print p_stops, p_names, p_strands
raise
if len(p_stops) > min_read_count:
avg = int(round(sum(p_stops) / float(len(p_stops))))
# write out reads in this cluster, using avg as coordinate
outfile.writelines('\t'.join([p_chrom, str(max(0, avg-1)), str(avg),
n_name, '0', n_strand]) + '\n'
for n_name, n_strand in zip(p_names, p_strands))
if outfile_pileup is not None:
outfile_pileup.write('\t'.join([p_chrom, str(max(0, avg-1)), str(avg),
p_names[0], str(len(p_stops)),
p_strands[0]]) + '\n')
# reset our record
p_chrom = chrom
p_stops = [stop]
p_names = [name]
p_strands = [strand]
# otherwise, the next read is within the window, on same chrom
else:
p_stops.append(stop)
p_names.append(name)
p_strands.append(strand)
# output anything left in queue after EOF
if len(p_stops) > 0:
avg = int(round(sum(p_stops) / float(len(p_stops))))
# write out reads in this cluster, using avg as coordinate
outfile.writelines('\t'.join([chrom, str(max(0, avg-1)), str(avg),
n_name, '0', n_strand]) + '\n'
for n_name, n_strand in zip(p_names, p_strands))
if outfile_pileup is not None:
outfile_pileup.write('\t'.join([chrom, str(max(0, avg-1)), str(avg),
p_names[0], str(len(p_stops)),
p_strands[0]]) + '\n')
if outfile_pileup is not None:
outfile_pileup.close()
outfile.close()