def main():
opts = get_options()
iterative_mapping()
## PARSE FASTA
genome = parse_fasta(opts.fasta if len(opts.fasta) <= 1 else opts.fasta[0],
chr_names=opts.chr_name, verbose=True)
def main():
opts = get_options()
iterative_mapping()
## PARSE FASTA
genome = parse_fasta(opts.fasta if len(opts.fasta) <= 1 else opts.fasta[0],
chr_names=opts.chr_name,
verbose=True)
def make_matrices(left_reads_fastq, right_reads_fastq, reads_fastq, genome_fasta, genome_index, \
output_directory, output_prefix, enzyme, res, chromosomes, threads_number, \
clean_tmp, tmp_dir):
print 'Begin to process reads.'
left_reads = ''
right_reads = ''
if reads_fastq != '': # left and right reads are stored in one file
range_start_left, range_stop_left, \
range_start_right, range_stop_right = calc_left_right_ranges(reads_fastq)
print 'Reads: ', reads_fastq
left_reads = reads_fastq
right_reads = reads_fastq
else: # left and right reads are stored separately
range_start_left, range_stop_left, \
range_start_right, range_stop_right = calc_range(left_reads_fastq)
print 'Left reads: ', left_reads_fastq
print 'Right reads: ', right_reads_fastq
print 'Output prefix: ', output_prefix
left_reads = left_reads_fastq
right_reads = right_reads_fastq
print 'Reference genome FASTA: ', genome_fasta
print 'Reference genome GEM index:', genome_index
print 'Output directory: ', output_directory
print 'Temp directory: ', tmp_dir
print 'Enzyme: ', enzyme
print 'Resolution: ', res, 'bp'
print 'Number of threads: ', threads_number
print 'Start pos for left reads: ', range_start_left
print 'Stop pos for left reads: ', range_stop_left
print 'Start pos for right reads: ', range_start_right
print 'Stop pos for right reads: ', range_stop_right
stdout.flush()
# map left reads to reference genome
out_sam_left_name = splitext(basename(left_reads))[0] + '_left.sam'
out_sam_left_path = join(output_directory, out_sam_left_name)
print 'Iterative mapping of left reads (using ' + str(threads_number) + ' threads)...'
stdout.flush()
sams_left = iterative_mapping(genome_index, left_reads, out_sam_left_path, \
range_start_left, range_stop_left, nthreads=threads_number,
temp_dir=tmp_dir)
print 'Done.'
stdout.flush()
# map right reads to reference genome
out_sam_right_name = splitext(basename(right_reads))[0] + '_right.sam'
out_sam_right_path = join(output_directory, out_sam_right_name)
print 'Iterative mapping of right reads (using ' + str(threads_number) + ' threads)...'
stdout.flush()
sams_right = iterative_mapping(genome_index, right_reads, out_sam_right_path, \
range_start_right, range_stop_right, nthreads=threads_number,
temp_dir=tmp_dir)
print 'Done.'
stdout.flush()
# load reference genome sequence
print 'Load reference genome sequence...'
stdout.flush()
chroms = chromosomes[:]
genome_seq = parse_fasta(genome_fasta, chr_names=chroms)
print 'Done.'
stdout.flush()
# create files with information about every left and right read
# and about their placement with respect to restriction sites
tsv_left_name = splitext(basename(left_reads))[0] + '_left.tsv'
tsv_left = join(output_directory, tsv_left_name)
tsv_right_name = splitext(basename(right_reads))[0] + '_right.tsv'
tsv_right = join(output_directory, tsv_right_name)
print 'Get information about restriction sites and reads placement...'
stdout.flush()
parse_sam(sams_left, sams_right, tsv_left, tsv_right, genome_seq, enzyme, \
verbose=True, ncpus=8)
print 'Done.'
stdout.flush()
# create file with both left and right reads that uniquelly mapped to reference genome
if reads_fastq != '': # left and right reads are stored in one file
common_reads_prefix = splitext(basename(reads_fastq))[0]
else: # left and right reads are stored separately
common_reads_prefix = output_prefix
uniq_reads_name = common_reads_prefix + '_both_map_uniq.tsv'
uniq_reads = join(output_directory, uniq_reads_name)
print 'Merge info about left and right reads in one file...'
stdout.flush()
get_intersection(tsv_left, tsv_right, uniq_reads, verbose=True)
print 'Done.'
stdout.flush()
# find read IDs that are filtered by default TADbit filters
print 'Mask reads...'
stdout.flush()
# debug
print "uniq_reads =", uniq_reads
masked = filter_reads(uniq_reads)
print 'Done.'
stdout.flush()
# apply all filters (exclude reads that were filtered)
print 'Filter masked reads...'
stdout.flush()
filtered_reads_name = common_reads_prefix + '_filtered.tsv'
filtered_reads = join(output_directory, filtered_reads_name)
apply_filter(uniq_reads, filtered_reads, masked)
print 'Done.'
stdout.flush()
# create matrices (one matrix per chromosome)
print 'Create Hi-C maps (one per chromosome)...'
stdout.flush()
hic_map(filtered_reads, resolution=res, by_chrom='intra', savedata=output_directory)
print 'Done.'
stdout.flush()
print 'Add resolution (' + str(resolution) + ') to matrix filenames...'
stdout.flush()
add_resolution(chromosomes, resolution, output_directory)
print 'Done.'
stdout.flush()
print 'Add headers to matrix files...'
stdout.flush()
add_headers(chromosomes, resolution, output_directory)
print 'Done.'
stdout.flush()
if clean_tmp: # Remove all SAM and TSV files from the output directory
print 'Remove SAM and TSV files from the output directory.'
stdout.flush()
map(os.remove, glob.glob(out_sam_left_path + '*'))
map(os.remove, glob.glob(out_sam_right_path + '*'))
map(os.remove, glob.glob(join(output_directory, '*.tsv')))
print 'Done.'
stdout.flush()
# print 'read 2'
# mapping(gem_index_path, fastq, out_map_dir2, 'HindIII',
# temp_dir=temp_dir2, windows=((100, 200),))
from pytadbit.mapping.mapper import iterative_mapping
from pytadbit.mapping.full_mapper import full_mapping
from pytadbit.parsers.map_parser import parse_map
from pytadbit.parsers.sam_parser import parse_sam
from pytadbit.parsers.genome_parser import parse_fasta
from pytadbit.mapping.mapper import get_intersection
from pytadbit.mapping.filter import filter_reads, apply_filter
if mapper == 1:
print 'read 1'
outfiles1 = iterative_mapping(gem_index_path, fastq, out_map_dir1,
r_beg1, [e + 2 for e in r_end1],
temp_dir=temp_dir1)
print 'read 2'
outfiles2 = iterative_mapping(gem_index_path, fastq, out_map_dir2,
r_beg2, [e + 2 for e in r_end2],
temp_dir=temp_dir2)
parse_thing = parse_sam
elif mapper == 2:
print 'read 1'
outfiles1 = full_mapping(gem_index_path, fastq, out_map_dir1, 'HindIII',
temp_dir=temp_dir1, frag_map=False,
windows=(zip(*(r_beg1, r_end1))))
print 'read 2'
outfiles2 = full_mapping(gem_index_path, fastq, out_map_dir2, 'HindIII',
temp_dir=temp_dir2, frag_map=False,
windows=(zip(*(r_beg2, r_end2))))
rep = 'SRR_test'
INFILE = INFILE % rep
OUTPATH = PATH + rep + '_' + str(chunk) + '/'
chr_names = ['2L', '2R', '3L', '3R', '4', 'X']
genome_seq = parse_fasta([PATH + 'dmel_reference/chr%s.fa' % crm for crm in chr_names], chr_names)
frags = map_re_sites('HindIII', genome_seq, verbose=True)
sams1 = iterative_mapping(
gem_index_path = PATH + 'dmel_reference/dm3.genome.gem',
fastq_path = INFILE,
out_sam_path = OUTPATH + '%s_r1.txt' % rep,
temp_dir = PATH + 'tmp_dir/',
range_start = [10] * 5, # starts with a flag sequence
range_stop = range(30, 55, 5),
nthreads = 8, # on intel corei7 CPUs 4 threads are as fast as
# 8, but leave some room for you other applications
max_reads_per_chunk = chunk,
single_end = True)
print 'created thes SAM files:', sams1
sams2 = iterative_mapping(
gem_index_path = PATH + 'dmel_reference/dm3.genome.gem',
fastq_path = INFILE,
out_sam_path = OUTPATH + '%s_r2.txt' % rep,
temp_dir = PATH + 'tmp_dir/',
range_start = range(80, 55, -5), # starts with a flag sequence
range_stop = [100] * 5,
nthreads = 8, # on intel corei7 CPUs 4 threads are as fast as
def make_matrices(left_reads_fastq, right_reads_fastq, reads_fastq, genome_fasta, genome_index, \
output_directory, output_prefix, enzyme, res, chromosomes, threads_number, \
clean_tmp, tmp_dir):
print 'Begin to process reads.'
left_reads = ''
right_reads = ''
if reads_fastq != '': # left and right reads are stored in one file
range_start_left, range_stop_left, \
range_start_right, range_stop_right = calc_left_right_ranges(reads_fastq)
print 'Reads: ', reads_fastq
left_reads = reads_fastq
right_reads = reads_fastq
else: # left and right reads are stored separately
range_start_left, range_stop_left, \
range_start_right, range_stop_right = calc_range(left_reads_fastq)
print 'Left reads: ', left_reads_fastq
print 'Right reads: ', right_reads_fastq
print 'Output prefix: ', output_prefix
left_reads = left_reads_fastq
right_reads = right_reads_fastq
print 'Reference genome FASTA: ', genome_fasta
print 'Reference genome GEM index:', genome_index
print 'Output directory: ', output_directory
print 'Temp directory: ', tmp_dir
print 'Enzyme: ', enzyme
print 'Resolution: ', res, 'bp'
print 'Number of threads: ', threads_number
print 'Start pos for left reads: ', range_start_left
print 'Stop pos for left reads: ', range_stop_left
print 'Start pos for right reads: ', range_start_right
print 'Stop pos for right reads: ', range_stop_right
stdout.flush()
# map left reads to reference genome
out_sam_left_name = splitext(basename(left_reads))[0] + '_left.sam'
out_sam_left_path = join(output_directory, out_sam_left_name)
print 'Iterative mapping of left reads (using ' + str(
threads_number) + ' threads)...'
stdout.flush()
sams_left = iterative_mapping(genome_index, left_reads, out_sam_left_path, \
range_start_left, range_stop_left, nthreads=threads_number,
temp_dir=tmp_dir)
print 'Done.'
stdout.flush()
# map right reads to reference genome
out_sam_right_name = splitext(basename(right_reads))[0] + '_right.sam'
out_sam_right_path = join(output_directory, out_sam_right_name)
print 'Iterative mapping of right reads (using ' + str(
threads_number) + ' threads)...'
stdout.flush()
sams_right = iterative_mapping(genome_index, right_reads, out_sam_right_path, \
range_start_right, range_stop_right, nthreads=threads_number,
temp_dir=tmp_dir)
print 'Done.'
stdout.flush()
# load reference genome sequence
print 'Load reference genome sequence...'
stdout.flush()
chroms = chromosomes[:]
genome_seq = parse_fasta(genome_fasta, chr_names=chroms)
print 'Done.'
stdout.flush()
# create files with information about every left and right read
# and about their placement with respect to restriction sites
tsv_left_name = splitext(basename(left_reads))[0] + '_left.tsv'
tsv_left = join(output_directory, tsv_left_name)
tsv_right_name = splitext(basename(right_reads))[0] + '_right.tsv'
tsv_right = join(output_directory, tsv_right_name)
print 'Get information about restriction sites and reads placement...'
stdout.flush()
parse_sam(sams_left, sams_right, tsv_left, tsv_right, genome_seq, enzyme, \
verbose=True, ncpus=8)
print 'Done.'
stdout.flush()
# create file with both left and right reads that uniquelly mapped to reference genome
if reads_fastq != '': # left and right reads are stored in one file
common_reads_prefix = splitext(basename(reads_fastq))[0]
else: # left and right reads are stored separately
common_reads_prefix = output_prefix
uniq_reads_name = common_reads_prefix + '_both_map_uniq.tsv'
uniq_reads = join(output_directory, uniq_reads_name)
print 'Merge info about left and right reads in one file...'
stdout.flush()
get_intersection(tsv_left, tsv_right, uniq_reads, verbose=True)
print 'Done.'
stdout.flush()
# find read IDs that are filtered by default TADbit filters
print 'Mask reads...'
stdout.flush()
masked = filter_reads(uniq_reads)
print 'Done.'
stdout.flush()
# apply all filters (exclude reads that were filtered)
print 'Filter masked reads...'
stdout.flush()
filtered_reads_name = common_reads_prefix + '_filtered.tsv'
filtered_reads = join(output_directory, filtered_reads_name)
apply_filter(uniq_reads, filtered_reads, masked)
print 'Done.'
stdout.flush()
# create matrices (one matrix per chromosome)
print 'Create Hi-C maps (one per chromosome)...'
stdout.flush()
hic_map(filtered_reads,
resolution=res,
by_chrom='intra',
savedata=output_directory)
print 'Done.'
stdout.flush()
print 'Add resolution (' + str(resolution) + ') to matrix filenames...'
stdout.flush()
add_resolution(chromosomes, resolution, output_directory)
print 'Done.'
stdout.flush()
print 'Add headers to matrix files...'
stdout.flush()
add_headers(chromosomes, resolution, output_directory)
print 'Done.'
stdout.flush()
if clean_tmp: # Remove all SAM and TSV files from the output directory
print 'Remove SAM and TSV files from the output directory.'
stdout.flush()
remove(out_sam_left_path + '*')
remove(out_sam_right_path + '*')
remove(join(output_directory, '*.tsv'))
print 'Done.'
stdout.flush()