#!/usr/bin/env python
"""Parse the output of GNU time (gtime), along with a profile name ($item)
and write a tab-delimited row to stdout with the following fields:

1. Program name
2. Number of threads
3. The dataset - either an error rate (for simulated data) or a data type (WGBS or RNA-Seq)
4. Quality cutoff
5. Duration of program execution
6. Max CPU usage
7. Max memory usage
"""
import argparse
from common import fileopen, parse_profile
import re

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument("-i", "--input", default="-")
    parser.add_argument("-o", "--output", default="-")
    parser.add_argument("-p", "--profile")
    args = parser.parse_args()

    prog, prog2, threads, dataset, qcut = parse_profile(args.profile)
    
    with fileopen(args.input, 'rt') as i:
        lines = [line.strip() for line in i.readlines()]

    cpu = lines[3]
    cpu_match = re.match("Percent of CPU this job got: (\\d+)%", cpu)
    assert cpu_match is not None
    cpu_pct = float(cpu_match.group(1))

    wc_time = lines[4]
    wc_match_prefix = "Elapsed \\(wall clock\\) time \\(h:mm:ss or m:ss\\): "
    wc_match = re.match(wc_match_prefix + "(?:(\\d+)h )?(\\d+)m ([\\d\\.]+)s", wc_time)
    if wc_match is None:
        wc_match = re.match(wc_match_prefix + "(?:(\\d+):)?(\\d+):([\\d\\.]+)", wc_time)
    assert wc_match is not None
    hrs = int(wc_match.group(1) or 0)
    mins = int(wc_match.group(2))
    secs = float(wc_match.group(3))
    duration = ':'.join((
        '{:02d}'.format(hrs),
        '{:02d}'.format(mins),
        '{:0.2f}'.format(secs)))
    duration_secs = (hrs * 3600) + (mins * 60) + secs

    memory = lines[9]
    memory_match = re.match("Maximum resident set size \\(kbytes\\): (\\d+)", memory)
    assert memory_match is not None
    memory_mbytes = int(memory_match.group(1)) / 1000

    with fileopen(args.output, "wt") as out:
        print(prog, prog2, threads, dataset, qcut, duration_secs,
        cpu_pct, memory_mbytes, sep="\t", file=out)

if __name__ == "__main__":
    main()
#!/usr/bin/env python
"""Parse the output of GNU time (gtime), along with a profile name ($item)
and write a tab-delimited row to stdout with the following fields:

1. Program name
2. Number of threads
3. The dataset - either an error rate (for simulated data) or a data type (WGBS or RNA-Seq)
4. Quality cutoff
5. Duration of program execution
6. Max CPU usage
7. Max memory usage
"""
import argparse
from common import fileopen, parse_profile
import re

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument("-i", "--input", default="-")
    parser.add_argument("-o", "--output", default="-")
    parser.add_argument("-p", "--profile")
    args = parser.parse_args()

    prog, prog2, threads, dataset, qcut = parse_profile(args.profile)
    
    with fileopen(args.input, 'rt') as i:
        lines = [line.strip() for line in i.readlines()]

    cpu = lines[3]
    cpu_match = re.match("Percent of CPU this job got: (\\d+)%", cpu)
    assert cpu_match is not None
    cpu_pct = float(cpu_match.group(1))

    wc_time = lines[4]
    wc_match_prefix = "Elapsed \\(wall clock\\) time \\(h:mm:ss or m:ss\\): "
    wc_match = re.match(wc_match_prefix + "(?:(\\d+)h )?(\\d+)m ([\\d\\.]+)s", wc_time)
    if wc_match is None:
        wc_match = re.match(wc_match_prefix + "(?:(\\d+):)?(\\d+):([\\d\\.]+)", wc_time)
    assert wc_match is not None
    hrs = int(wc_match.group(1) or 0)
    mins = int(wc_match.group(2))
    secs = float(wc_match.group(3))
    duration = ':'.join((
        '{:02d}'.format(hrs),
        '{:02d}'.format(mins),
        '{:0.2f}'.format(secs)))
    duration_secs = (hrs * 3600) + (mins * 60) + secs

    memory = lines[9]
    memory_match = re.match("Maximum resident set size \\(kbytes\\): (\\d+)", memory)
    assert memory_match is not None
    memory_mbytes = int(memory_match.group(1)) / 1000

    with fileopen(args.output, "wt") as out:
        print(prog, prog2, threads, dataset, qcut, duration_secs,
        cpu_pct, memory_mbytes, sep="\t", file=out)

if __name__ == "__main__":
    main()
#!/usr/bin/env python Parse the output of GNU time (gtime), along with a profile name ($item) and write a tab-delimited row to stdout with the following fields:  1. Program name 2. Number of threads 3. The dataset - either an error rate (for simulated data) or a data type (WGBS or RNA-Seq) 4. Quality cutoff 5. Duration of program execution 6. Max CPU usage 7. Max memory usage