parsing_opts.py 文件源码

def parsing_plot_orf_density():
    parser = argparse.ArgumentParser(
        description="This script is designed for plot the P-site profile of specified ORF."
    )
    parser.add_argument("-a","--annot_dir",dest="annot_dir",required=True,type=str,
                        help="transcripts annotation directory, generated by prepare_transcripts.")
    parser.add_argument("-c","--config_file",dest="config_file",required=True,
                        help="defile bam file information in this file, \
                        please refer to the example file in data folder.",type=str)
    parser.add_argument("-t","--transcript_id",dest="transcript_id",required=True,type=str,
                        help="the transcript id")
    parser.add_argument("-s","--orf_tstart",dest="orf_tstart",required=True,type=int,
                        help="transcript-level coordinates of start of ORF (orf_tstart)")
    parser.add_argument("-e","--orf_tstop",dest="orf_tstop",required=True,type=int,
                        help="transcript-level coordinates of end of ORF (orf_tstop)")
    parser.add_argument("-o","--outname",dest="outname",required=False,type=str,default="",
                        help="output file name,default is transcriptid_tstart_tstop.pdf")
    parser.add_argument('-V',"--version",action="version",version=__version__)
    args = parser.parse_args()

    args.orf_tstart = args.orf_tstart -1 # change to 0 based
    if not os.path.exists(args.annot_dir):
        raise ValueError("Error, the transcript annotation directory not found: {} \n \
                     pls run prepare_transcripts.py first. ".format(args.annot_dir))
    return args