本文整理汇总了Python中pysam.AlignedRead方法的典型用法代码示例。如果您正苦于以下问题：Python pysam.AlignedRead方法的具体用法？Python pysam.AlignedRead怎么用？Python pysam.AlignedRead使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类pysam的用法示例。
在下文中一共展示了pysam.AlignedRead方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: __init__
# 需要导入模块: import pysam [as 别名]
# 或者: from pysam import AlignedRead [as 别名]
def __init__(self, line, start=-1, end=-1, strand=1,
file_format='', bamfile=None, info=''):
self.info = ""
self.file_format = file_format
if type(line) == pysam.AlignedRead or type(line) == pysam.AlignedSegment:
self.load_pysamread(line, bamfile)
elif start == -1:
self.load_line(line, file_format)
elif end == -1:
self.load_pos(line, start, start, strand)
else:
self.load_pos(line, start, end, strand)
if len(info) > 0:
self.info = info 示例2: load_pysamread
# 需要导入模块: import pysam [as 别名]
# 或者: from pysam import AlignedRead [as 别名]
def load_pysamread(self, line, bamfile):
if bamfile is None:
raise "Interval of pysam AlignedRead without bamfile"
self.chrom = line.reference_name
self.start = line.reference_start
self.end = line.reference_end
if line.is_reverse:
self.strand = -1
else:
self.strand = 1 示例3: dropest_bc_correct
# 需要导入模块: import pysam [as 别名]
# 或者: from pysam import AlignedRead [as 别名]
def dropest_bc_correct(bamfilepath: str, dropest_out: str, corrected_output: str) -> None:
"""Using the output of DropEst:
(1) Corrects barcodes directly in the bam file
(2) Produces a valid barcodes list
BAMFILEPATH - bam file with sorted reads obtained running DropEst
DROPEST-OUT - R dump `rds` file generated by DropEst
"""
try:
import rpy2.robjects as ro
from velocyto.r_interface import convert_r_obj
except:
ImportError("A problem was encountered importing rpy2. To run this `velocyto tools` rpy2 and R need to be installed (the use conda is recommended)")
# bamfilepath = sys.argv[1]
# filename = os.path.join(parentpath, f"{bamfilename.split('_')[0]}_dropEst.rds")
parentpath, bamfilename = os.path.split(bamfilepath)
filename = dropest_out
logging.info(f"Loading `merge_targets` from {filename} using R / rpy2")
mapping = convert_r_obj(ro.r(f"rds <- readRDS('{filename}'); rds$merge_targets")) # a dict
output_path = os.path.join(parentpath, f"barcodes_{bamfilename.split('_')[0]}.tsv")
logging.info(f"Generating {output_path}")
with open(output_path, "w") as fout:
unique_bcs = set(list(mapping.values()))
str_ = '\n'.join(list(unique_bcs))
fout.write(str_)
infile = pysam.AlignmentFile(bamfilepath, mode="rb")
if corrected_output is None:
bam_out_path = os.path.join(parentpath, f"correct_{bamfilename}")
else:
bam_out_path = corrected_output
outfile = pysam.AlignmentFile(bam_out_path, mode="wb", template=infile)
for read in infile:
# read: pysam.AlignedRead
cb = read.get_tag("CB")
if cb in mapping:
read.set_tag("CB", mapping[cb], value_type="Z")
outfile.write(read)
infile.close()
outfile.close()
logging.info("Done")
return