ctb

Figure out what kmer(s) match a given hash

Usage:

./get-kmers-for-hashes.py data/GCF_000005845.2_ASM584v2_genomic.fna.gz 31 9061051479453

ctb

class: sourmash_signature
email: ''
filename: 0Hour_ATCACG_L002001.1.fq
hash_function: 0.murmur64
signatures:
- abundances: [1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 1, 1, 1, 95, 1, 1,
    1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 1,
    1, 1, 2, 1, 1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 1, 1, 4, 1, 1, 1, 1, 1, 2, 2, 1,
    3, 1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 2, 1, 1, 2, 1, 1,
    2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 1, 2,

ctb

Some stuff on sourmash

Note: currently uses the ctb branch of dib-lab/sourmash.

ctb

Here, the .get function on maps is about 1m times slower than the .getitem function. Why?

To run (requires Python 3, Cython, and a C/C++ build environment):

python setup.py build_ext -i
python test.py

ctb

If you post this URL into mybinder.org, you’ll get a running notebook (well, two clicks in -) https://github.com/ctb/2016-carole

Intro to binder: http://ivory.idyll.org/blog/2016-mybinder.html

Proposal outlining some thoughts around future tech dev for binder:

• http://ivory.idyll.org/blog/2016-mybinder-workshop-proposal.html and
• https://github.com/dib-lab/2016-binder-proposal-to-sloan

ctb

SPG=../../spacegraphcats

all: acido-sim-catlas acido-genome-catlas acido-reads-catlas

clean:
	./make-sim-catlas.py acido-chunk-reads data/acido-chunk[12].fa.gz --clean
	./make-genome-catlas.py acido-genome data/acido-chunk[12].fa.gz --clean
	./recover-reads.py acido-chunk-reads data/acido-chunk1.fa.sig.dump.txt \
		acido-chunk1.reads.fa.abundtrim acido-chunk1-1.extract.fa --clean
	./recover-reads.py acido-chunk-reads data/acido-chunk1.fa.sig.dump.txt \

ctb

import random
import timeit
dna = ['A', 'C', 'G', 'T'] * 10000
random.seed(1)
random.shuffle(dna)
dna = "".join(dna)

import khmer
print(khmer)
kh = khmer._Nodegraph(31, [1])

ctb

output from:

for i in 0 1 2 3 4 5;
do
   ../../sourmash/sourmash search_mxt 15genome.catlas.5.mxt *.sig -l $i \
       > /tmp/level${i}.txt
done

ctb

> If only I were evil-er, I could be the Darth Vader of
> bioinformatics! "I find your publication attempts... disturbing."

    "Don't be too proud of this technological terror you've
constructed. The ability to platform a workflow is insignificant
next to the power of the Source."

ctb

Keybase proof

I hereby claim:

• I am ctb on github.
• I am ctitusbrown (https://keybase.io/ctitusbrown) on keybase.
• I have a public key whose fingerprint is 5CE0 DDA2 1061 A2E7 BB00 730F 994F 75DD D6C8 935B

To claim this, I am signing this object: