Moderator: Matt Shirley
Matt Shirley ♦ 7.9k
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- Cambridge, MA
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- http://mattshirley.com/
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- mdshw5
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- Last seen:
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- Joined:
- 6 years, 6 months ago
- Email:
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Posts by Matt Shirley
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... 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 25 days ago by
Matt Shirley ♦ 7.9k
0
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3
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236
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3
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... 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 27 days ago by
Matt Shirley ♦ 7.9k
1
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5
answers
271
views
5
answers
Answer:
A: chrom.sizes computed locally
... $ pip install pyfaidx
$ faidx -i chromsizes input.fa > output.chromsizes ...
written 4 weeks ago by
Matt Shirley ♦ 7.9k
2
votes
4
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306
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4
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... FOUR! 🏌⛳️
$ python -c "import sys; [sys.stdout.write('>'+str(i)+'\n'+seq) for i, seq in enumerate(sys.stdin)]" ...
written 5 weeks ago by
Matt Shirley ♦ 7.9k
1
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4
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306
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4
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... I think you want `sys.stdout.write` ...
written 5 weeks ago by
Matt Shirley ♦ 7.9k
0
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2
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661
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2
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... 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 5 weeks ago by
Matt Shirley ♦ 7.9k
0
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2
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229
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2
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... You can do this with [pyfaidx](https://github.com/mdshw5/pyfaidx#faidx) as well.
$ pip install pyfaidx
$ faidx -m -b regions.bed file.fa # mask with "N"
$ faidx -s X -m -b regions.bed file.fa # mask with "X"
$ faidx -M -b regions.bed file.fa # soft-mask with lowercase characters
...
written 7 weeks ago by
Matt Shirley ♦ 7.9k
1
vote
2
answers
450
views
2
answers
... You just need to add a '\n' at the end of the string using the write method. ...
written 8 weeks ago by
Matt Shirley ♦ 7.9k
1
vote
2
answers
450
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2
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... You can use `pyfaidx` to do this in one step:
$ pip install pyfaidx
$ faidx -x -e "lambda x: x + '_sample1'" test.fasta
The `faidx` script is comparable to the `pyfasta` script, but has [many more](https://github.com/mdshw5/pyfaidx#faidx) features. It also creates/uses the `.fai` index, ju ...
written 8 weeks ago by
Matt Shirley ♦ 7.9k
1
vote
3
answers
373
views
3
answers
Answer:
A: faidx implementation with C++
... You already have some pretty good answers, but I wanted to point out that I've done a Python implementation here: https://github.com/mdshw5/pyfaidx/blob/master/pyfaidx/__init__.py#L537
There's a lot of object-oriented stuff to get around, but the docstring explains the logic behind fetching a subse ...
written 8 weeks ago by
Matt Shirley ♦ 7.9k
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