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#!/usr/bin/env python
"""Convert time stamps from bcbio logs into hourly timings per step.
/path/to/bcbio/anaconda/python your_work_dir/log/bcbio-nextgen.log
This parses out the "Timing" steps in the log file to provide timing
per analysis block. If your analysis had a lot of stops and restarts,
you'll need to manually reconstruct a reasonable estimate of timings
around the stops/failures. The best approach is to get a file of Timinig
only data with `grep Timing log/bcbio-nextgen.log` then manually add in
failure/stop points with timestamps and "unexpected error" for the
import sys
import arrow
from tabulate import tabulate
def main(log_file):
prev_time = None
total_time = None
cur_process = None
vals = []
with open(log_file) as in_handle:
for line in in_handle:
if line.strip() and line.find("Timing:") > 0 or line.lower().find("unexpected error") > 0:
cur_time = arrow.get(line.split("]")[0])
if prev_time:
tdiff = cur_time - prev_time
if cur_process.lower().find("unexpected error") == -1:
if total_time:
total_time += tdiff
total_time = tdiff
if cur_process.lower().find("unexpected error") == -1:
vals.append([cur_process, str(tdiff).replace(":00", "")])
cur_process = line.split(":")[-1].strip()
prev_time = cur_time
header = ["Total", str(total_time).replace(":00", "")]
print tabulate(vals, header, tablefmt="orgtbl")
if __name__ == "__main__":