Moderator: John

gravatar for John
John11k
Reputation:
10,960
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Location:
Germany
Website:
http://at.cg/
Last seen:
2 hours ago
Joined:
5 years, 6 months ago
Email:
m***********@gmail.com

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Posts by John

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Comment: C: Poll: How many people have PyPy?
... Well, the typical alternative is that I just make an if/else branch that checks the interpreter type. I did this in a previous tool that can use array.array (CPython), Numpy (both, but need numpy) or CFFI (PyPy) to store the array, whatever the user has installed - but the result was a real mess to ...
written 4 days ago by John11k
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Comment: C: Poll: How many people have PyPy?
... You don't *need* it installed, but for a Python tool developer it is very useful to know how many people have access to a PyPy environment. There are a few times where i have thought "oh, i could write this function to be 1 minute in CPython, and 10 seconds in pypy, or i could write it to be 2 minut ...
written 4 days ago by John11k
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Comment: C: uQ - small binary FASTQ
... Hey Brian! sorry for the 4 day delay, i have been frantically writing up this tool in a small section in my thesis, and i thought it would perhaps be best if I sent you the link to those pages so you can totally get it, since i know the README doesn't cover the specifics much, and the code is possib ...
written 5 days ago by John11k
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Comment: C: Lossless ALAPY Fastq Compressor (now with stdin/stdout support)
... Sorry lh3, it wasn't your fault - 5 weeks ago the README for uQ wasn't very good, so i'm not surprised it didn't work out. When you run --test and don't specify a --compressor, uQ optimizes for smallest *uncompressed* file size (for in-memory applications). The uQ file in your tests is *uncompresse ...
written 12 days ago by John11k
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Comment: C: why does this pipe work
... It's because the stuff after the | isn't being fed to a command, or rather, it's being fed to a null command, the output of which (which is nothing) is sent to tmp. So the 1>tmp bit is working exactly as you expect, it's just that there's an invisible null command between the | and the 1. "true" ...
written 12 days ago by John11k
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Comment: C: Collaboration on an empirical QC tool
... That would be great Michael! OK so i'll get to work on tidying up the code base and producing modules for the proposed statistics. For some stats there's more than one way to calculate it (e.g. duplication rate could be based on sequence or on mapping position, and the distinction is purely subjec ...
written 12 days ago by John11k
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Answer: A: Collaboration on an empirical QC tool
... It sounds like you're thinking along the same lines as SeQC: https://github.com/JohnLonginotto/seqc Going through your list, SeQC is: - collaborative by design, in that SeQC servers are designed to be networked together to share stat data. - all stats are pre-computed. It's a stat database after ...
written 14 days ago by John11k
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Answer: A: why does this pipe work
... To do this without using samtools, you can do something like: https://gist.github.com/JohnLonginotto/2112cc0a054f6244983348e83a24d5ad Also note, this method of detecting file integrity, which is ultimately what a truncated file is, is bad. One should validate the BAM fully, and then produce a chec ...
written 16 days ago by John11k
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Comment: C: Good practices while dealing with very large datasets
... It's ok. I think this is just something we're not going to agree about, and i'll also admit I was a bit over the top. Try and look at it from my side, I see questions like this (https://www.biostars.org/p/251456/) regularly, and I know there's no way to debug this. Streams happened. The error went d ...
written 21 days ago by John11k
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Comment: C: A long run time problem
... I've **totally** stolen jrj.healey's solution, and made it faster by using defaultdict, storing things in tuples, and only uppercasing the things you need. Also, if you really want your mind blown, try running it in [PyPy][1] :) It will probably take *seconds*. import csv import argparse ...
written 21 days ago by John11k

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