davidliwei

#!/usr/bin/env python
'''
Automatically estimate insert size of the paired-end reads for a given SAM/BAM file.
Usage: getinsertsize.py <SAM file> or samtools view <BAM file> | getinsertsize.py -
Author: Wei Li

Copyright (c) <2015> <Wei Li>

davidliwei

#!/bin/env python3

import os
import re
import sys

if len(sys.argv)<2:
        print('This script extracts insert size information from Cufflinks logs.',file=sys.stderr);
        print('Usage: getinsertsize [cufflinks log file]',file=sys.stderr);
        print('Note: you may specify different log files using filename wildcards.',file=sys.stderr);

davidliwei

#!/usr/bin/env python3
'''
gtf2bed.py converts GTF file to BED file.
Usage: gtf2bed.py {OPTIONS} [.GTF file]

History
    Nov.5th 2012:
        1. Allow conversion from general GTF files (instead of only Cufflinks supports).
        2. If multiple identical transcript_id exist, transcript_id will be appended a string like "_DUP#" to separate.
'''