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…, after every interval dsa step. Also switch to f-strings for readability
FMakosza
reviewed
Oct 29, 2025
python/runNanoSeq.py
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| commands[i] = (cmd, ) | ||
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| with open(f"{tmpDir}/dsa/{i+1}.dsa.cmd", "w") as cmd_file: | ||
| cmd_file.write(cmd.replace(';', ';\n\n')) |
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Would it be cleaner to build cmd as a list of strings, then use "\n".join(cmd)? Semicolons may appear in filenames (which may warrant quoting all the path parameters!) and, while it isn't an issue in this script, they're also part of the awk syntax.
E.g.,
cmd.append(f"bgzip -f -l 2 \"{tmpDir}/dsa/{i+1}.dsa.bed\";\nsleep 2;\nbgzip -t \"{tmpDir}/dsa/{i+1}.dsa.bed.gz\";")
cmd.append(f"touch \"{tmpDir}/dsa/{i+1}.done\";")
[...]
cmd_file.write("\n".join(cmd))
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Initial steps to improve error surfacing in the DSA step