Moderator: Matt Shirley

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Matt Shirley6.9k
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mdshw5
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Posts by Matt Shirley

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Comment: C: GC Content of Fasta file --- Python Help
... As an aside, I think this is one of the problems with testing-as-an-interview-screen since the OP could have great biology or reasoning skills but just doesn't nail this specific problem. It's obvious that there's lots of logic in this python function, also understanding of the problem, and an infor ...
written 21 hours ago by Matt Shirley6.9k
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Comment: C: GC Content of Fasta file --- Python Help
... Agreed, although the last line does take care of the final sequence in the file. Still, lots of stuff in the code that reads like it was kind of dashed together from Stackoverflow posts. `gc = at = unknown = 0` is more commonly `gc, at, unknown = (0, 0, 0)`, although both are technically correct. Ho ...
written 21 hours ago by Matt Shirley6.9k
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Comment: C: Correct Way To Parse A Fasta File In Python
... That's because this is a generator function. Do get all headers you'll have to do something like: fasta = fasta_iter("hg19.fa") for header, seq in fasta: print(header) Or, you can use a package such as https://github.com/mdshw5/pyfaidx and do: from pyfaidx import Fasta fasta = Fasta("hg19 ...
written 6 days ago by Matt Shirley6.9k
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Answer: A: Is It Fastq Format
... It seems like you might need some basic Linux training. I suggest starting with the lessons at [software carpentry](http://swcarpentry.github.io/shell-novice/). For now, however, I have a suggestion: why don't you try your task using [Galaxy](http://usegalaxy.org)? I wrote the initial version of the ...
written 7 weeks ago by Matt Shirley6.9k
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Answer: A: Being co-first author for two nature series journals, what kinds of job can I fi
... If you're looking for a faculty position, my best advice would be to model your career on a you professor/mentor you admire and that has a similar background to yourself. Approach them and ask how they achieved their position, and ask what they would do differently in today's funding and research cl ...
written 12 weeks ago by Matt Shirley6.9k
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Comment: C: Filtering fasta file based on identifier
... "standard out" or "stdout". You can redirect this to a file like: awk '/^>/{N=0} /^>P/{N=1} {if(N)print}' *.fa > out.fa ...
written 3 months ago by Matt Shirley6.9k
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Answer: A: I'm in need of a practice pileup file to test a program I'm making. Is there a p
... You might try `sra-pileup` from the NCBI [SRA toolkit](https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=sra-pileup). You can even just use some of the examples from the documentation like: sra-pileup -r SRR390728 > example.pileup ...
written 4 months ago by Matt Shirley6.9k
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Comment: C: Should We Release Database Dumps Of All Questions On Biostar?
... Was there ever a consensus reached about licensing content? How about licensing "meta" content such as tags? ...
written 4 months ago by Matt Shirley6.9k
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Comment: C: PileOMeth double counting when paired-end reads overlap?
... If you're worried about search indexing, I would suggest going to a memorable name (hopefully completely unique) and then associating that name with the appropriate terms on the GitHub readme file or project site. I'd note that "methylup" isn't taken (aside from maybe [this](http://www.therascienc ...
written 4 months ago by Matt Shirley6.9k
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Answer: A: how to return the componenets from PCA back to original variables?
... I don't believe this is possible. Principal components are derived from projecting the data to a vector that maximizes the spread or variance along that vector - [see here](http://stats.stackexchange.com/a/140579) mostly the visualizations. Asking which variables contributed most to this projection ...
written 4 months ago by Matt Shirley6.9k

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Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Not having root access sucks; installing software without root privileges
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: What Does 2X250Bp Buy Us?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How To Select Only One Human Genome Build (Hg19) From The Encode Project'S Data
Popular Question 10 months ago, created a question with more than 1,000 views. For Troubling Trends In Scientific Software Use
Appreciated 10 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Appreciated 10 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How To Select Only One Human Genome Build (Hg19) From The Encode Project'S Data
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