Sam Nicholls SamStudio8
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| """ | |
| Provides functions for the purpose of parsing a Sun Grid Engine (SGE) | |
| accounting file for job metadata. | |
| """ | |
| __author__ = "Sam Nicholls <msn@aber.ac.uk>" | |
| __copyright__ = "Copyright (c) Sam Nicholls" | |
| __version__ = "0.0.32" | |
| __maintainer__ = "Sam Nicholls <msn@aber.ac.uk>" |
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| y3 = [86,90,90,68,86,79,79,78,61,62,45,60] | |
| y2 = [81,81,79,79,77,73,55,55,86,84,83,81] | |
| # 8 modules per band | |
| BAND_SIZE = 8 | |
| BAND_DELTA = len(y3) - BAND_SIZE | |
| # Extract BAND_SIZE best year 3 modules | |
| y3_sorted = sorted(y3) | |
| band_3 = y3_sorted[-BAND_SIZE:] |
SamStudio8
/ awk
Last active
August 29, 2015 14:07
Benchmarking reads over a pair of 42GB FASTQ files (~1.5 billion lines)
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| # awk 3.1.7 | |
| # 1hr 1m | |
| awk '$1 ~ /@/ {++c} END {print c}' $1 | |
| # 1hr 1m | |
| awk '/^@/ {c++} END {print c}' $1 | |
| # 55m | |
| awk '{if (substr($0,0,1) == "@") { ++c }} END {print c}' $1 |
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