Moderator: Matt Shirley

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Matt Shirley7.9k
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Cambridge, MA
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http://mattshirley.com/
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mdshw5
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6 years, 6 months ago
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Posts by Matt Shirley

<prev • 680 results • page 1 of 68 • next >
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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 25 days ago by Matt Shirley7.9k
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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 27 days ago by Matt Shirley7.9k
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Answer: A: chrom.sizes computed locally
... $ pip install pyfaidx $ faidx -i chromsizes input.fa > output.chromsizes ...
written 4 weeks ago by Matt Shirley7.9k
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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 5 weeks ago by Matt Shirley7.9k
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Comment: C: Convert sequence file to fasta format using python
... I think you want `sys.stdout.write` ...
written 5 weeks ago by Matt Shirley7.9k
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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 5 weeks ago by Matt Shirley7.9k
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Answer: A: Consensus fasta file with uncovered bases set to Ns
... 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 Shirley7.9k
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Comment: C: Add filename to fasta headers of multiple fasta files inside loop
... You just need to add a '\n' at the end of the string using the write method. ...
written 8 weeks ago by Matt Shirley7.9k
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Answer: A: Rename headers of multiple fasta files inside loop
... 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 Shirley7.9k
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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 Shirley7.9k

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