def _realign_bam(bam_fpath, reference_fpath, out_bam_fpath, threads=False):
'It realigns the bam using GATK Local realignment around indels'
# reference sam index
_create_sam_reference_index(reference_fpath)
# reference picard dict
_create_picard_dict(reference_fpath)
# bam index
index_bam(bam_fpath)
# the intervals to realign
# gatk_dir = get_setting("GATK_DIR")
# gatk_jar = os.path.join(gatk_dir, 'GenomeAnalysisTK.jar')
gatk_jar = get_setting('GATK_JAR')
intervals_fhand = NamedTemporaryFile(suffix='.intervals')
stderr = NamedTemporaryFile(suffix='picard.stderr')
stdout = NamedTemporaryFile(suffix='picard.stdout')
cmd = ['java', '-jar', gatk_jar, '-T', 'RealignerTargetCreator',
'-I', bam_fpath, '-R', reference_fpath, '-o', intervals_fhand.name]
check_call(cmd, stderr=stderr, stdout=stdout)
# the realignment itself
cmd = ['java', '-jar', gatk_jar, '-I', bam_fpath, '-R', reference_fpath,
'-T', 'IndelRealigner', '-targetIntervals', intervals_fhand.name,
'-o', out_bam_fpath]
if threads and threads > 1:
cmd.extend(['-nt', str(get_num_threads(threads))])
check_call(cmd, stderr=stderr, stdout=stdout)
intervals_fhand.close()
def _create_picard_dict(fpath):
'It creates a picard dict if if it does not exist'
dict_path = os.path.splitext(fpath)[0] + '.dict'
if os.path.exists(dict_path):
return
picard_jar = get_setting("PICARD_JAR")
cmd = ['java', '-jar', picard_jar, 'CreateSequenceDictionary',
'R=%s' % fpath,
'O=%s' % dict_path]
stderr = NamedTemporaryFile(suffix='picard.stderr')
check_call(cmd, stderr=stderr)
def merge_sams(in_fpaths, out_fpath):
picard_jar = get_setting("PICARD_JAR")
cmd = ['java', '-jar', picard_jar, 'MergeSamFiles',
'O={}'.format(out_fpath)]
for in_fpath in in_fpaths:
cmd.append('I={}'.format(in_fpath))
stderr = NamedTemporaryFile(suffix='picard.stderr')
stdout = NamedTemporaryFile(suffix='picard.stdout')
try:
check_call(cmd, stderr=stderr, stdout=stdout)
except CalledProcessError:
sys.stderr.write(open(stderr.name).read())
sys.stdout.write(open(stdout.name).read())
def sort_bam(in_bam_fpath, out_bam_fpath=None):
if out_bam_fpath is None:
out_bam_fpath = in_bam_fpath
if out_bam_fpath == in_bam_fpath:
sorted_fhand = NamedTemporaryFile(suffix='.sorted.bam', delete=False)
temp_out_fpath = sorted_fhand.name
else:
temp_out_fpath = out_bam_fpath
picard_jar = get_setting("PICARD_JAR")
cmd = ['java', '-jar', picard_jar, 'SortSam',
'INPUT={0}'.format(in_bam_fpath),
'OUTPUT={0}'.format(temp_out_fpath),
'SORT_ORDER=coordinate', 'VALIDATION_STRINGENCY=LENIENT']
stderr = NamedTemporaryFile(suffix='picard.stderr')
check_call(cmd, stderr=stderr)
if temp_out_fpath != out_bam_fpath:
shutil.move(temp_out_fpath, out_bam_fpath)
import pysam
try:
from pysam.csamtools import Samfile
except ImportError:
from pysam import Samfile
from crumbs.statistics import (draw_histogram_ascii, IntCounter, LABELS,
BestItemsKeeper)
from bam_crumbs.settings import get_setting
from bam_crumbs.utils.flag import SAM_FLAG_BINARIES, SAM_FLAGS
from bam_crumbs.utils.bin import get_binary_path
from collections import Counter
# pylint: disable=C0111
DEFAULT_N_BINS = get_setting('DEFAULT_N_BINS')
DEFAULT_N_MOST_ABUNDANT_REFERENCES = get_setting(
'DEFAULT_N_MOST_ABUNDANT_REFERENCES')
def count_reads(ref_name, bams, start=None, end=None):
'It returns the count of aligned reads in the region'
count = 0
for bam in bams:
count += bam.count(reference=ref_name, start=start, end=end)
return count
class ArrayWrapper(object):
'A thin wrapper around numpy to have the same interface as IntCounter'
try:
from pysam.csamtools import Samfile
except ImportError:
from pysam import Samfile
from crumbs.statistics import (draw_histogram_ascii, IntCounter, LABELS,
BestItemsKeeper)
from bam_crumbs.settings import get_setting
from bam_crumbs.utils.flag import SAM_FLAG_BINARIES, SAM_FLAGS
from bam_crumbs.utils.bin import get_binary_path
from collections import Counter
# pylint: disable=C0111
DEFAULT_N_BINS = get_setting('DEFAULT_N_BINS')
DEFAULT_N_MOST_ABUNDANT_REFERENCES = get_setting('DEFAULT_N_MOST_ABUNDANT_REFERENCES')
def count_reads(ref_name, bams, start=None, end=None):
'It returns the count of aligned reads in the region'
count = 0
for bam in bams:
count += bam.count(reference=ref_name, start=start, end=end)
return count
class ArrayWrapper(object):
'A thin wrapper around numpy to have the same interface as IntCounter'
def __init__(self, array, bins=DEFAULT_N_BINS):
self.array = array
