上面的代码示例中,我们首先读取了BAM文件example.bam,然后计算了reads的数量,并输出到控制台。 关系图 BAM_FILEREADSContains 在关系图中,BAM文件包含reads,是一对多的关系。 类图 BAM_FILE- filename: character+readBam(filename) : BamFileREADS- reads_count: numeric+getReadsCount() : numeric 在类图中,BAM...
Example BAM filedoi:10.6084/M9.FIGSHARE.1460736.V1C. Frederik
import pysam # 打开BAM文件 bam_file = pysam.AlignmentFile("example.bam", "rb") # 遍历文件中的每一条记录 for read in bam_file.fetch(): # 检查是否满足特定条件,例如特定的序列ID if read.query_name == "sequence_id_to_search": print(read.tostring()) # 关闭文件 bam_file.close() ...
For example, a string ‘10A5^AC6’ means from the leftmost reference base in the alignment, there are 10 matches followed by an A on the reference which is difffferent from the aligned read base; the next 5 reference bases are matches followed by a 2bp deletion from the reference; the...
有关详细信息,请参阅 。 mkdir build cd build cmake .. make # Executable is bin/bam-readcount 用法 不带参数运行命令行帮助: $ bam-readcount Usage: bam-readcount [OPTIONS][region] Generate metrics for bam_file at single nucleotide positions. Example: bam-readcount -f ref.f ...
I noticed that in the Release Notes of the 2013a bioinformatics toolbox it is mentioned that now it is possible to write BAM files, but I couldn't find any example. Could someone give me a simple example of using the new feature. For example if I have a BAM file with the ScannedDict...
$ bam-readcount Usage: bam-readcount [OPTIONS] <bam_file> [region] Generate metrics for bam_file at single nucleotide positions. Example: bam-readcount -f ref.fa some.bam Available options: -h [ --help ] produce this message -v [ --version ] output the version number -q [ --min...
(107349540 bases). in this example, the only reference sequence contig was chromosome 14, but most reference genomes will have several contigs and several @sq lines to match. the second line starts with @pg, indicating that it describes the program used to generate the sam file (and ...
To export a list of customers, enter command “1”. This will produce a CSV similar to the below example.The exported list of customers will be available in the “output” file of the tool’s folders.View exported customers in the file “customers.csv”. For each cust...
Usage:bam-readcount[OPTIONS]<bam_file>[region]Generatemetricsforbam_file at single nucleotide positions.Example:bam-readcount-fref.fa some.bamAvailableoptions:-h[--help]producethismessage-v[--version]output the version number-q[--min-mapping-quality]arg(=0)minimum mapping quality of reads used...