def processBed(inbed, col, posF, posS, delimeter, outbasename):
logging.info("Creating BedTool object.")
myBedTool = BedTool(inbed)
logging.info("Retrieving feature length.")
bedobj = myBedTool.each(addFeatureLengthToScoreCol, col, posF, posS,
delimeter).saveas(outbasename + ".bed")
plotFeaturesLength(bedobj, col, posF, posS, delimeter, outbasename)
def promoter(bed, n, genome, delimiter, index, out):
if os.path.exists(out):
os.remove(out)
gnm_d = process_genome(genome)
bedobj = BedTool(bed)
bedobj.each(check_name_col)
fnames_list = [f.name.split(delimiter)[index] for f in bedobj]
previous_g, previous_f, firstLine, obj_idx, nrecords = "", "", True, 0, len(
bedobj)
with open(out, 'w') as outfile:
for f in bedobj:
gname = get_feature_name(f.name, delimiter, index)
if obj_idx == len(
fnames_list) - 1: #if last line [index checking will fail]
if gname != previous_g and f.strand == "+":
outfile.write(add_bp_positive_feature(f, n))
elif f.strand == "+":
outfile.write(str(f))
elif f.strand == "-":
outfile.write(add_bp_negative_feature(f, n, gnm_d))
elif gname != previous_g and f.strand == "+":
outfile.write(add_bp_positive_feature(f, n))
elif gname != previous_g and obj_idx != nrecords and fnames_list[
obj_idx +
1] == gname: # first feature of multifeature gene in negative strand
outfile.write(str(f))
elif gname != previous_g: # if negative gene has only one feature
outfile.write(add_bp_negative_feature(f, n, gnm_d))
elif gname == previous_g and f.strand == "+" or obj_idx != nrecords and fnames_list[
obj_idx +
1] == gname: # if positive strand or not last feature of negative gene
outfile.write(str(f))
elif gname == previous_g and fnames_list[
obj_idx +
1] != gname: #if last feature of a negative strand gene
outfile.write(add_bp_negative_feature(f, n, gnm_d))
obj_idx += 1
previous_g = gname
outfile.close()
def processIntronicBed(inbed,lengths,outbasename,featureType):
logging.info("Creating BedTool object.")
myBedTool = BedTool(inbed)
logging.info("Writing " + featureType + " length.")
bedobj=myBedTool.each(addIntronLengthToScoreCol).saveas(outbasename + ".bed")
plotIntrons(bedobj,outbasename,featureType,0)
for l in lengths:
smallIntObj=bedobj.each(filterByLength,l).saveas(outbasename + "_smaller" + str(l) + ".bed")
plotIntrons(smallIntObj,outbasename,featureType,l)
def get_merged_exons(genes, gtf, genome_fasta, strand):
'''
get all exons from specified genes, merging any
overlapping exonic regions, also return their
respective sequences in a dictionary object
'''
gene_gtf = gtf[gtf.gene.isin(genes)]
if len(gene_gtf) == 0:
return pd.DataFrame(), {}
gene_gtf = gene_gtf.drop('gene', axis=1)
gene_strand = gene_gtf.strand.values[0]
strand = gene_strand if strand == '' else strand
with tempfile.NamedTemporaryFile(mode='r+') as temp_gtf:
gene_gtf.to_csv(temp_gtf.name, index=False, header=False, sep='\t')
# load gene GTF info, extract and merge exons
g = BedTool(temp_gtf.name)
exons = BedTool(subset_featuretypes(g, 'exon'))
exons = exons.remove_invalid().sort().merge()
exseq = exons.each(add_strand, strand)
exseq = exseq.sequence(fi=genome_fasta, s=True)
block_seqs = get_block_seqs(exseq)
blocks = pd.DataFrame()
with tempfile.NamedTemporaryFile(mode='r+') as temp_exons:
exons.saveas(temp_exons.name)
blocks = pd.read_csv(temp_exons,
header=None,
sep='\t',
names=['chr', 'start', 'end'])
if type(genes) == str:
blocks['name'] = genes
else:
blocks['name'] = genes[0] # use first gene as representative
blocks['score'] = '.'
blocks['strand'] = strand
blocks['chr'] = blocks['chr'].map(str)
blocks.start = blocks.start.map(int)
blocks.end = blocks.end.map(int)
block_names = []
# reverse numbering if the gene is on the reverse strand
if gene_strand == '-':
block_names = [
'|' + str(i) for i in reversed(range(1,
len(blocks) + 1))
]
else:
block_names = ['|' + str(i) for i in range(1, len(blocks) + 1)]
blocks['name'] = blocks['name'] + block_names
return (blocks, block_seqs)
elif args.verbose:
logging.basicConfig(level=logging.INFO,
format="%(filename)s - %(levelname)s - %(message)s")
else:
logging.basicConfig(format="%(filename)s - %(levelname)s - %(message)s")
logging.info("Parsed arguments:")
if args.outfile:
logging.info(" outfile: enabled writing to file")
logging.info(" outfile: '{}'".format(args.outfile))
logging.info(" outfile: '{}'".format(args.outfile))
logging.info("")
# data processing
alns = BedTool(args.infile)
# select either from 5' or 3'-end
if args.threeprime:
clnts = alns.each(three_prime, upstream=0, downstream=1)
else:
clnts = alns.each(five_prime, upstream=1, downstream=0)
# write to file or to stdout
if args.outfile:
clnts.saveas(args.outfile)
else:
tmptool = clnts.saveas()
logging.debug("results written to temporary file :" + tmptool.fn)
tmp = open(tmptool.fn)
for line in tmp:
stdout.write(line)
tmp.close()
# first flank the introns by $flank either side
def flank_introns(feature):
feature.start = feature.start - int(flank)
feature.end = feature.end + int(flank)
return(feature)
#if not os.path.exists(os.path.dirname(outFile)):
# os.mkdir(os.path.dirname(outFile))
#if not outFile.endswith("csv"):
# outFile = outFile + "_" + str(flank) + "_coverage.csv"
# flank each intron by 100 to capture exons either side
flanked = introns.each(flank_introns)
# intersect the flanked introns with the iCLIP clusters
#intersect = introns.intersect(clusters, s=True,wa=True, wb = True)
intersect = flanked.intersect(clusters, s=stranded,wa=True, wb = True)
print type(intersect)
# store as dictionary
intervals = dict()
for feature in intersect:
coord = str(feature.chrom) + ":" + str(feature.start) + "-" + str(feature.stop)
length = int(feature.stop) - int(feature.start)
strand = str(feature.strand)
start_pos = int(feature.start)
if coord not in intervals:
logging.basicConfig(level=logging.DEBUG, format="%(asctime)s - %(filename)s - %(levelname)s - %(message)s")
elif args.verbose:
logging.basicConfig(level=logging.INFO, format="%(filename)s - %(levelname)s - %(message)s")
else:
logging.basicConfig(format="%(filename)s - %(levelname)s - %(message)s")
logging.info("Parsed arguments:")
if args.outfile:
logging.info(" outfile: enabled writing to file")
logging.info(" outfile: '{}'".format(args.outfile))
logging.info(" outfile: '{}'".format(args.outfile))
logging.info("")
# data processing
alns = BedTool(args.infile)
# select either from 5' or 3'-end
if args.threeprime:
clnts = alns.each(three_prime, upstream=0, downstream=1)
else:
clnts = alns.each(five_prime, upstream=1, downstream=0)
# write to file or to stdout
if args.outfile:
clnts.saveas(args.outfile)
else:
tmptool = clnts.saveas()
logging.debug("results written to temporary file :" + tmptool.fn)
tmp = open(tmptool.fn)
for line in tmp:
stdout.write(line)
tmp.close()
feature.strand = "+"
return (feature)
elif feature.strand == "+":
feature.end = feature.start
feature.start = feature.start - 10
# switch strand
feature.strand = "-"
return (feature)
else:
print "feature must be + or - "
return (feature)
print("getting flanking coordinates")
downstream = clusters.each(get_downstream_sequence)
# get fasta sequence for each coordinate
print("retrieving genomic sequences")
fasta = downstream.sequence(fi=reference, s=True, tab=True)
# apply tests. 1. is there a stretch of 6*A or are there 7 A in any order?
print("testing each cluster for A-rich sequence")
# random_primers = []
# test = []
# with open(fasta.seqfn, "r") as f:
# for line in f:
# seq = line.strip().upper().split("\t")[1]
# if "AAAAAA" in seq or seq.count("A") >= 7:
for fup, core, fdown in izip(fup_reader, core_reader, fdown_reader):
assert fup[0] == core[0] == fdown[
0], "Error: sequence ids of cores and flanks don't match."
# setup fasta headers and sequences
fa_header = ">" + core[0]
seq_viewpoint = fup[1].lower() + core[1].upper() + fdown[1].lower()
# seq_normal = fup[1].upper() + core[1].upper() + fdown[1].upper()
viewpointfa.write(fa_header + "\n")
viewpointfa.write(seq_viewpoint + "\n")
viewpointfa.close()
# prepare input coordinates
bsites = BedTool(args.bsites_fn).sort().saveas()
centers = bsites.each(midpoint).saveas()
# prepare positive instances
logging.info("preparing positive instances")
if (args.chromosome_limits):
logging.debug("using chromosome_limits " + args.chromosome_limits)
cores = centers.slop(
s=True,
l=int(args.core_length / 2),
# -1 to account for the center nucleotide!
r=int(args.core_length / 2) + (args.core_length % 2) - 1,
g=args.chromosome_limits).each(offset_zero_by_one).saveas(
pos_core_bed_fn)
else:
cores = centers.slop(
s=True,
core_reader = reader(core_tabseq, delimiter="\t")
fdown_reader = reader(fdown_tabseq, delimiter="\t")
for fup, core, fdown in izip(fup_reader, core_reader, fdown_reader):
assert fup[0] == core[0] == fdown[0], "Error: sequence ids of cores and flanks don't match."
# setup fasta headers and sequences
fa_header = ">" + core[0]
seq_viewpoint = fup[1].lower() + core[1].upper() + fdown[1].lower()
# seq_normal = fup[1].upper() + core[1].upper() + fdown[1].upper()
viewpointfa.write(fa_header + "\n")
viewpointfa.write(seq_viewpoint + "\n")
viewpointfa.close()
# prepare input coordinates
bsites = BedTool(args.bsites_fn).sort().saveas()
centers = bsites.each(midpoint).saveas()
# prepare positive instances
logging.info("preparing positive instances")
if (args.chromosome_limits):
logging.debug("using chromosome_limits " + args.chromosome_limits)
cores = centers.slop(s=True,
l=int(args.core_length / 2),
# -1 to account for the center nucleotide!
r=int(args.core_length / 2) +
(args.core_length % 2) - 1,
g=args.chromosome_limits).each(offset_zero_by_one).saveas(pos_core_bed_fn)
else:
cores = centers.slop(s=True,
l=int(args.core_length / 2),
# -1 to account for the center nucleotide!
def subset(bed, n, keep_small, out):
print("Applying subset")
bedobj = BedTool(bed)
bedobj.each(apply_subset, n, keep_small).saveas(out)
#!/usr/bin/env python
import os
import sys
import subprocess
sys.path.insert(0,'/mnt/lustre/home/cusanovich/Programs/lib/python2.6/site-packages/pybedtools-0.6.2-py2.6-linux-x86_64.egg/pybedtools')
from pybedtools import BedTool, featurefuncs
windowsize = 10000
windowname = str(windowsize/1000) + 'kb'
indir = '/mnt/lustre/home/cusanovich/Kd_Arrays/GenomeAnnotations/StartAnnots/'
outdir = '/mnt/lustre/home/cusanovich/Kd_Arrays/GenomeAnnotations/FinalAnnots/'
annots = ['GSE31388_eQtlTable_cleaned.bed','sorted_PritchardQTLs_merged.bed','gwascatalog_ucsc_merged.bed']
#annots = ['GSE31388_eQtlTable_cleaned.bed']
jacked = BedTool('/mnt/lustre/home/cusanovich/centipede/hg19_jack_centipede_sorted_pwms_clean.bed')
tss = BedTool('/mnt/lustre/home/cusanovich/Kd_Arrays/Centipede/Annotation/HT12ensemblTSScombinedsorted.bed')
for annot in annots:
print annot
currannot = BedTool(indir + annot)
currout = annot.split('.')[0]
print 'Intersecting...'
inter = jacked.intersect(currannot,wa=True,wb=True).moveto(outdir + windowname + '_' + currout + '_centipede_intersect.bed')
inter = BedTool(outdir + windowname + '_' + currout + '_centipede_intersect.bed')
print 'Calculating midpoints...'
intermid = inter.each(featurefuncs.midpoint).moveto(outdir + windowname + '_' + currout + '_centipede_intersect_midpoint.bed')
print 'Finding TSSs...'
inter = BedTool(outdir + windowname + '_' + currout + '_centipede_intersect_midpoint.bed')
outter = tss.window(intermid,w=windowsize).moveto(outdir + windowname + '_' + currout + '_insite.bed')
def main(use_config=True,
bed1=None,
bed2=None,
method=None,
tempdir=None,
md=None,
largewindow=None,
scanner=None,
debug=False,
label1=None,
label2=None,
jobid=None):
'''This is the main script of the combine function that is called within
TFEA. Default arguments are assigned to variables within config.vars.
Parameters
----------
use_config : boolean
Whether to use a config module to assign variables.
bed1 : list
A list of strings specifying full paths to bed files corresponding to
a single condition (replicates)
bed2 : list
A list of strings specifying full paths to bed files corresponding to
a single condition (replicates)
method : str
Method for combining input bed files into a single bed file
tempdir : str
Full path to a directory where files will be saved
md : boolean
Whether md-score bed files are generated
largewindow : int
Half-length of window size to use when generating md-score related
bed files
scanner : str
Scanner method to use in SCANNER module. Only needed if md also
specified. If equal to 'genome hits', md bed files generated will be
only contain one base and be centered at the middle of the region
Returns
-------
None - Assigns varaibles within config if use_config set to True
Raises
------
FileEmptyError
If any resulting file is empty
'''
start_time = time.time()
if use_config:
bed1 = config.vars['BED1']
bed2 = config.vars['BED2']
method = config.vars['COMBINE']
tempdir = config.vars['TEMPDIR']
md = config.vars['MD']
md_bedfile1 = config.vars['MD_BEDFILE1']
md_bedfile2 = config.vars['MD_BEDFILE2']
largewindow = config.vars['LARGEWINDOW']
scanner = config.vars['SCANNER']
label1 = config.vars['LABEL1']
label2 = config.vars['LABEL2']
debug = config.vars['DEBUG']
jobid = config.vars['JOBID']
print("Combining Regions...", end=' ', flush=True, file=sys.stderr)
if md_bedfile1 and md_bedfile2:
centered_md_bedfile1 = tempdir / 'md_bedfile1.centered.bed'
centered_md_bedfile2 = tempdir / 'md_bedfile2.centered.bed'
md = md and (not md_bedfile1 or not md_bedfile2
) #Boolean to determine whether to generate MD bed files
md_pybedtool1 = BedTool(str(md_bedfile1))
md_pybedtool1.each(center_feature).each(
extend_feature,
size=largewindow).remove_invalid().saveas(centered_md_bedfile1)
md_pybedtool2 = BedTool(str(md_bedfile2))
md_pybedtool2.each(center_feature).each(
extend_feature,
size=largewindow).remove_invalid().saveas(centered_md_bedfile2)
if use_config:
config.vars['MD_BEDFILE1'] = centered_md_bedfile1
config.vars['MD_BEDFILE2'] = centered_md_bedfile2
#Use MuMerge to merge bed files
if method == 'mumerge':
mumerge_input = tempdir / 'mumerge_input.txt'
combined_file = tempdir / 'combined_file.mumerge'
#Write MuMerge input file
# with open(mumerge_input, 'w') as F:
# F.write("#file\tsampid\tgroup\n")
# for i,bedpath in enumerate(bed1, 1):
# F.write(f'{bedpath}\t{label1}{i}\t{label1}\n')
# for i,bedpath in enumerate(bed2, 1):
# F.write(f'{bedpath}\t{label2}{i}\t{label2}\n')
#MuMerge Command - output to combined_file.mumerge.bed
combined_file = mumerge(mumerge_input,
combined_file,
bed1=bed1,
bed2=bed2,
label1=label1,
label2=label2)
clean_combined_file = tempdir / 'combined_file.mumerge.clean.bed'
combined_pybedtool = BedTool(str(combined_file))
combined_pybedtool.remove_invalid().saveas(clean_combined_file)
combined_file = clean_combined_file
# combined_file = Path(str(combined_file) + '_MUMERGE.bed')
#Perform simple merge same as merge all for md bed files
if md:
md_bedfile1 = tempdir / "md_bedfile1.mumerge"
md_mumerge_input1 = tempdir / "md_mumerge_input1.txt"
md_bedfile1 = mumerge(md_mumerge_input1,
md_bedfile1,
bed1=bed1,
label1=label1,
label2=label2)
md_pybedtool1 = BedTool(str(md_bedfile1))
md_bedfile1 = tempdir / "md_bedfile1.mumerge.final.bed"
md_pybedtool1.each(center_feature).each(
extend_feature,
size=largewindow).remove_invalid().saveas(md_bedfile1)
md_bedfile2 = tempdir / "md_bedfile2.mumerge"
md_mumerge_input2 = tempdir / "md_mumerge_input2.txt"
md_bedfile2 = mumerge(md_mumerge_input2,
md_bedfile2,
bed2=bed2,
label1=label1,
label2=label2)
md_pybedtool2 = BedTool(str(md_bedfile2))
md_bedfile2 = tempdir / "md_bedfile2.mumerge.final.bed"
md_pybedtool2.each(center_feature).each(
extend_feature,
size=largewindow).remove_invalid().saveas(md_bedfile2)
# md_merged_bed1 = merge_bed(beds=bed1).each(featurefuncs.extend_fields, 4)
# md_merged_bed2 = merge_bed(beds=bed2).each(featurefuncs.extend_fields, 4)
# md_merged_bed1.each(center_feature).each(extend_feature, size=largewindow).remove_invalid().saveas(md_bedfile1)
# md_merged_bed2.each(center_feature).each(extend_feature, size=largewindow).remove_invalid().saveas(md_bedfile2)
#Merge all bed regions, for MD merge condition replicates
elif method == 'mergeall':
combined_file = tempdir / "combined_file.mergeall.bed"
merged_bed = merge_bed(beds=bed1 + bed2)
# merged_bed.each(center_feature).each(extend_feature, size=largewindow).saveas(combined_file)
merged_bed.remove_invalid().saveas(combined_file)
if md:
md_bedfile1 = tempdir / "md_bedfile1.merge.bed"
md_bedfile2 = tempdir / "md_bedfile2.merge.bed"
# md_merged_bed1 = merge_bed(beds=bed1).each(featurefuncs.extend_fields, 4).each(featurefuncs.rename, '1')
# md_merged_bed2 = merge_bed(beds=bed2).each(featurefuncs.extend_fields, 4).each(featurefuncs.rename, '1')
md_merged_bed1 = merge_bed(beds=bed1).each(
featurefuncs.extend_fields, 4)
md_merged_bed2 = merge_bed(beds=bed2).each(
featurefuncs.extend_fields, 4)
md_merged_bed1.each(center_feature).each(
extend_feature,
size=largewindow).remove_invalid().saveas(md_bedfile1)
# md_merged_bed1.saveas(md_bedfile1)
md_merged_bed2.each(center_feature).each(
extend_feature,
size=largewindow).remove_invalid().saveas(md_bedfile2)
# md_merged_bed2.saveas(md_bedfile2)
elif method == 'tfitclean':
# combined_file = tfit_clean(beds=bed1+bed2, tempdir=tempdir)
combined_file = tempdir / "combined_file.tfitclean.bed"
size_cut = 200
cleaned_bed = clean_bed(beds=bed1 + bed2, size_cut=size_cut)
# cleaned_bed.each(center_feature).each(extend_feature, size=largewindow).saveas(combined_file)
cleaned_bed.remove_invalid().saveas(combined_file)
if md:
md_bedfile1 = tempdir / "md_bedfile1.clean.bed"
md_bedfile2 = tempdir / "md_bedfile2.clean.bed"
md_cleaned_bed1 = clean_bed(beds=bed1)
md_cleaned_bed2 = clean_bed(beds=bed2)
# md_cleaned_bed1.each(center_feature).each(extend_feature, size=largewindow).saveas(md_bedfile1)
md_cleaned_bed1.saveas(combined_file)
# md_cleaned_bed2.each(center_feature).each(extend_feature, size=largewindow).saveas(md_bedfile2)
md_cleaned_bed2.saveas(combined_file)
#Intersect all bed regions, for MD intersect condition replicates
elif method == 'intersectall':
combined_file = tempdir / 'combined_file.intersectall.bed'
intersected_bed = intersect_bed(beds=bed1 + bed2)
# intersected_bed.each(center_feature).each(extend_feature, size=largewindow).saveas(combined_file)
intersected_bed.remove_invalid().saveas(combined_file)
if md:
md_bedfile1 = tempdir / "md_bedfile1.intersect.bed"
md_bedfile2 = tempdir / "md_bedfile2.intersect.bed"
md_intersected_bed1 = intersect_bed(beds=bed1)
md_intersected_bed2 = intersect_bed(beds=bed2)
md_intersected_bed1.each(center_feature).each(
extend_feature,
size=largewindow).remove_invalid().saveas(md_bedfile1)
# md_intersected_bed1.saveas(combined_file)
md_intersected_bed2.each(center_feature).each(
extend_feature,
size=largewindow).remove_invalid().saveas(md_bedfile2)
# md_intersected_bed2.saveas(combined_file)
#Merge all regions, filter small regions. For MD perform this for each condition
elif method == 'tfitremovesmall':
# combined_file = tfit_remove_small(beds=bed1+bed2, tempdir=tempdir)
size_cut = 200
combined_file = tempdir / "combined_file.mergeallnosmall.bed"
merged_bed = merge_bed(beds=bed1 + bed2)
# merged_bed.filter(lambda b: b.stop - b.start > size_cut).each(center_feature).each(extend_feature, size=largewindow).saveas(combined_file)
merged_bed.filter(lambda b: b.stop - b.start > size_cut).saveas(
combined_file)
if md:
md_bedfile1 = tempdir / "md_bedfile1.merge.bed"
md_bedfile2 = tempdir / "md_bedfile2.merge.bed"
md_merged_bed1 = merge_bed(beds=bed1)
md_merged_bed2 = merge_bed(beds=bed2)
# md_merged_bed1.filter(lambda b: b.stop - b.start > size_cut).each(center_feature).each(extend_feature, size=largewindow).saveas(md_bedfile1)
md_merged_bed1.filter(
lambda b: b.stop - b.start > size_cut).saveas(combined_file)
# md_merged_bed2.filter(lambda b: b.stop - b.start > size_cut).each(center_feature).each(extend_feature, size=largewindow).saveas(md_bedfile2)
md_merged_bed2.filter(
lambda b: b.stop - b.start > size_cut).saveas(combined_file)
#Intersect replicates, merge conditions. For MD intersect condition replicates
elif method == 'intersect/merge':
# combined_file = intersect_merge_bed(bed1=bed1, bed2=bed2, tempdir=tempdir)
combined_file = tempdir / 'combined_file.intermerge.bed'
intersected_bed1 = intersect_bed(beds=bed1)
intersected_bed2 = intersect_bed(beds=bed2)
merged_bed = intersected_bed1.cat(intersected_bed2).merge().sort()
# merged_bed.each(center_feature).each(extend_feature, size=largewindow).saveas(combined_file)
merged_bed.remove_invalid().saveas(combined_file)
if md:
md_bedfile1 = tempdir / "md_bedfile1.intersect.bed"
md_bedfile2 = tempdir / "md_bedfile2.intersect.bed"
md_intersected_bed1 = intersect_bed(beds=bed1).each(
featurefuncs.extend_fields, 4).each(featurefuncs.rename, '1')
md_intersected_bed2 = intersect_bed(beds=bed2).each(
featurefuncs.extend_fields, 4).each(featurefuncs.rename, '1')
md_intersected_bed1.each(center_feature).each(
extend_feature,
size=largewindow).remove_invalid().saveas(md_bedfile1)
# md_intersected_bed1.saveas(md_bedfile1)
md_intersected_bed2.each(center_feature).each(
extend_feature,
size=largewindow).remove_invalid().saveas(md_bedfile2)
# md_intersected_bed2.saveas(md_bedfile2)
else:
raise exceptions.InputError("Error: COMBINE option not recognized.")
#Check to make sure no files are empty
if os.stat(combined_file).st_size == 0:
raise exceptions.FileEmptyError(
"Error in COMBINE module. Resulting bed file is empty.")
if md:
if os.stat(md_bedfile1).st_size == 0 or os.stat(
md_bedfile2).st_size == 0:
raise exceptions.FileEmptyError(
"Error in COMBINE module. Resulting md bed file is empty.")
if use_config:
#Assign MD_BEDFILE variables in config
config.vars['MD_BEDFILE1'] = md_bedfile1
config.vars['MD_BEDFILE2'] = md_bedfile2
#Assign COMBINED_FILE variable in config
if use_config:
config.vars['COMBINED_FILE'] = combined_file
#Record time, print
total_time = time.time() - start_time
if use_config:
config.vars['COMBINEtime'] = total_time
print("done in: " + str(datetime.timedelta(seconds=int(total_time))),
". Processing",
len(combined_file.read_text().split('\n')),
"regions",
file=sys.stderr)
if debug:
multiprocess.current_mem_usage(jobid)
def newber(binner,factor): """Returns bed record with all binding for a factor merged and renamed.""" newbie = BedTool(binner).sort().merge(nms=True).each(featurefuncs.midpoint) newbie = newbie.each(featurefuncs.rename,factor) return(newbie)