生信常用工具合集，包括gtf/fastx/bam/bed格式文件的处理和转换，bam,bed注释工具，R绘图脚本等

# pybiotk: A python toolkit for bioinformatics analysis ## Install ### use PyPi(official) ``` pip install pybiotk ``` **An older version may be installed** ### or ``` git clone https://gitee.com/liqiming_whu/pybiotk.git cd pybiotk pip install . ``` ## Modules ``` console_scripts = gtf2bed = pybiotk.convert.gtf2bed:run bed2bedgraph = pybiotk.convert.bed2bedgraph:run fq2fasta = pybiotk.convert.fq2fasta:run bam2fastx = pybiotk.convert.bam2fastx:run bampe_order_by_name = pybiotk.convert.bampe_order_by_name:run bam_random = pybiotk.utils.bam_random:run gtf_filter = pybiotk.utils.gtf_filter:run fasta_filter = pybiotk.utils.fasta_filter:run fastq_uniq = pybiotk.utils.fastq_uniq:run fastq_join = pybiotk.utils.fastq_join:run fastx_rename = pybiotk.utils.fastx_rename:run genomefetcher = pybiotk.utils.genomefetcher:run reverse_fastx = pybiotk.utils.reverse_fastx:run seq_random = pybiotk.utils.seq_random:run merge_row = pybiotk.utils.merge_row:run read_tables = pybiotk.utils.read_tables:run rmats_filter = pybiotk.utils.rmats_filter:run count_normalize = pybiotk.utils.normalize:run reference_count = pybiotk.utils.reference_count:run pyanno = pybiotk.utils.pyanno:run rna_fragment_size = pybiotk.utils.fragment_size:run merge_subseq = pybiotk.utils.merge_subseq:run subseq_analysis = pybiotk.utils.subseq_analysis:run ``` ## Usage ``` usage: pyanno [-h] -i INPUT -o OUTPUT -g GTF [-l {transcript,gene}] [--tss_region TSS_REGION [TSS_REGION ...]] [--downstream DOWNSTREAM] [-s] [--rule {1+-,1-+,2++,2--,1++,1--,2+-,2-+,+-,-+,++,--}] [-p] [--ordered_by_name] optional arguments: -h, --help show this help message and exit -i INPUT, --input INPUT input file, bam or bed. The file type will be inferred from the filename suffix ['*.bam', '*.bed']. (default: None) -o OUTPUT, --output OUTPUT output file name. (default: None) -g GTF, --gtf GTF gtf file download from Genecode, or a sorted gtf file. (default: None) -l {transcript,gene}, --level {transcript,gene} annotation level, transcript or gene. (default: transcript) --tss_region TSS_REGION [TSS_REGION ...] choose region from tss. (default: [-1000, 1000]) --downstream DOWNSTREAM downstream length from tes. (default: 3000) -s, --strand require same strandedness. (default: False) --rule {1+-,1-+,2++,2--,1++,1--,2+-,2-+,+-,-+,++,--} how read(s) were stranded during sequencing. only for bam. (default: 1+-,1-+,2++,2--) -p, --pair annotate fragments instead of reads. (default: False) --ordered_by_name if input bam is ordered by name, only for pair-end bam. (default: False) ```