Moderator: Matt Shirley

gravatar for Matt Shirley
Matt Shirley8.0k
Reputation:
7,980
Status:
Trusted
Location:
Cambridge, MA
Website:
http://mattshirley.com/
Twitter:
mdshw5
Scholar ID:
Google Scholar Page
Last seen:
11 hours ago
Joined:
6 years, 8 months ago
Email:
m*****@gmail.com

Posts by Matt Shirley

<prev • 684 results • page 1 of 69 • next >
3
votes
1
answer
511
views
1
answers
Comment: C: Call for requirement: a fast all-in-one FASTQ preprocessor (in C++, multi-thread
... To your point about multithreading, the operations you're proposing can be parallelized using unix paradigms of small programs that do one thing well and then: 1. Splitting files into chunks (we already do this routinely with FASTQ files) 2. Using pipes to operate on a data stream using multiple to ...
written 6 weeks ago by Matt Shirley8.0k
0
votes
1
answer
173
views
1
answers
Answer: A: How to fix Prokka`s annotation software error?
... Maybe post a bit of your file or the output from `grep -A1 SRR1181196.1 FastaSequences.fasta` ...
written 6 weeks ago by Matt Shirley8.0k
0
votes
1
answer
173
views
1
answers
Comment: C: How to fix Prokka`s annotation software error?
... Maybe post a bit of your file or the output from `grep -A1 SRR1181196.1 FastaSequences.fasta` ...
written 6 weeks ago by Matt Shirley8.0k
0
votes
1
answer
173
views
1
answers
Comment: C: How to fix Prokka`s annotation software error?
... Maybe post a bit of your file or the output from `grep -A1 SRR1181196.1 FastaSequences.fasta` ...
written 6 weeks ago by Matt Shirley8.0k
1
vote
3
answers
500
views
3
answers
Comment: C: Download SAM/BAM files from SRA takes ages!!!
... You can dump “spots” 1 through n using one process, and n through k using another process. Basically run fastq-dump on the same SRA archive but exporting a different chunk of the fastq file. This will scale until you run out of disk IO or CPU threads. ...
written 11 weeks ago by Matt Shirley8.0k
0
votes
3
answers
355
views
3
answers
Answer: A: Is there a way to fetch genomic sequences at given coordinates without downloadi
... There's a project called [genomepy](https://github.com/simonvh/genomepy) that handles the genome downloads and uses pyfaidx as the interface for queries. You could give that a shot, but you'd still be downloading files, just abstracting away the downloading process. ...
written 11 weeks ago by Matt Shirley8.0k
1
vote
5
answers
357
views
5
answers
Answer: A: chrom.sizes computed locally
... $ pip install pyfaidx $ faidx -i chromsizes input.fa > output.chromsizes ...
written 3 months ago by Matt Shirley8.0k
2
votes
4
answers
486
views
4
answers
Answer: A: Convert sequence file to fasta format using python
... FOUR! 🏌⛳️ $ python -c "import sys; [sys.stdout.write('>'+str(i)+'\n'+seq) for i, seq in enumerate(sys.stdin)]" ...
written 3 months ago by Matt Shirley8.0k
1
vote
4
answers
486
views
4
answers
Comment: C: Convert sequence file to fasta format using python
... I think you want `sys.stdout.write` ...
written 3 months ago by Matt Shirley8.0k
0
votes
2
answers
893
views
2
answers
Comment: C: FASTA file into excel file format?
... Not sure you can just change the extension to .xls, since .xls is some kind of binary file with more than just ASCII text. You can also use [pyfaidx](https://github.com/mdshw5/pyfaidx#faidx) to make a "transposed" FASTA file: faidx --transform transposed tests/data/genes.fasta AB821309.1 ...
written 3 months ago by Matt Shirley8.0k

Latest awards to Matt Shirley

Good Answer 3 days ago, created an answer that was upvoted at least 5 times. For A: How Can I Do Principal Components Analysis ?
Commentator 23 days ago, created a comment with at least 3 up-votes. For C: What Does 2X250Bp Buy Us?
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Popular Question 3 months ago, created a question with more than 1,000 views. For On the utility of publishing a tool paper
Scholar 3 months ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Scholar 4 months ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
Scholar 4 months ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Scholar 4 months ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: What Does 2X250Bp Buy Us?
Scholar 4 months ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
Appreciated 5 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Popular Question 5 months ago, created a question with more than 1,000 views. For On the utility of publishing a tool paper
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: How Can I Do Principal Components Analysis ?
Appreciated 6 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Appreciated 6 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Scholar 7 months ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
Popular Question 7 months ago, created a question with more than 1,000 views. For Comments Left Inappropriately As Answers To A Question
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1026 users visited in the last hour