add sourmash rules - Githubissues

I have 2 output files specified. need index to provide 1st one

On Thu, Sep 14, 2017 at 6:39 PM, Tomasz notifications@github.com wrote:

@tkosciol commented on this pull request.

In oecophylla/distance/sourmash.rule https://github.com/biocore/oecophylla/pull/74#discussion_r139048156:

expand(distance_dir + '{sample}/sourmash/{sample}.sig', sample=samples)

output:

distance_dir + 'combined_analysis/sourmash.similarity.csv',

distance_dir + 'combined_analysis/sourmash.dist.dm'

log:

distance_dir + "logs/sourmash_dm.log"

benchmark:

"benchmarks/distance/sourmash_dm.txt"

run:

from skbio.stats.distance import DistanceMatrix

from skbio.io import write

import pandas as pd

import numpy as np

shell('''

set +u; {params.env}; set -u

sourmash compare {i} --csv {output[0]}'.format(i=' '.join(input))

in shell() you don't need to specify {output[0]}, it should be simply {output}

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/biocore/oecophylla/pull/74#pullrequestreview-62928904, or mute the thread https://github.com/notifications/unsubscribe-auth/AA9CeIX076dFomsJ8bD48zRHrIq3OB_9ks5sidU9gaJpZM4PYYYX .

biocore / oecophylla

add sourmash rules #74

@tkosciol commented on this pull request.