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[MRG] remove lingering uses of sourmash_lib #626

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merged 3 commits into from
Jan 13, 2019
Merged

[MRG] remove lingering uses of sourmash_lib #626

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500fbb3
remove lingering uses of sourmash_lib
ctb Jan 12, 2019
26424dc
Merge branch 'master' into fix/sourmash_lib
luizirber Jan 13, 2019
0278afe
Merge branch 'master' into fix/sourmash_lib
luizirber Jan 13, 2019
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2 changes: 1 addition & 1 deletion benchmarks/benchmarks.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
from __future__ import unicode_literals

from screed.fasta import fasta_iter
from sourmash_lib._minhash import MinHash
from sourmash._minhash import MinHash
from tests.sourmash_tst_utils import get_test_data


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4 changes: 2 additions & 2 deletions tests/test_lca.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,8 +15,8 @@
from . import sourmash_tst_utils as utils
import sourmash

from sourmash_lib.lca import lca_utils
from sourmash_lib.lca.lca_utils import *
from sourmash.lca import lca_utils
from sourmash.lca.lca_utils import *

## lca_utils tests

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14 changes: 7 additions & 7 deletions utils/compute-dna-mh-another-way.py
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Expand Up @@ -35,16 +35,16 @@ def kmers(seq, k):

import sys, screed
import mmh3
import sourmash_lib
print('imported sourmash:', sourmash_lib, file=sys.stderr)
from sourmash_lib import MinHash
import sourmash_lib.signature
import sourmash
print('imported sourmash:', sourmash, file=sys.stderr)
from sourmash import MinHash
import sourmash.signature

record = next(iter(screed.open(sys.argv[1])))
print('loaded', record.name, file=sys.stderr)
revcomp = reverse(complement((record.sequence)))

mh = sourmash_lib.MinHash(ksize=K, n=500, is_protein=False)
mh = sourmash.MinHash(ksize=K, n=500, is_protein=False)

#
# compute the actual hashes to insert by breaking down the sequence
Expand All @@ -71,5 +71,5 @@ def kmers(seq, k):

mh.add_hash(hash)

s = sourmash_lib.signature.SourmashSignature('', mh, name=record.name)
print(sourmash_lib.signature.save_signatures([s]))
s = sourmash.signature.SourmashSignature('', mh, name=record.name)
print(sourmash.signature.save_signatures([s]))
14 changes: 7 additions & 7 deletions utils/compute-input-prot-another-way.py
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Expand Up @@ -67,15 +67,15 @@ def kmers(seq, k):

import sys, screed
import mmh3
import sourmash_lib
print('imported sourmash:', sourmash_lib, file=sys.stderr)
from sourmash_lib import MinHash
import sourmash_lib.signature
import sourmash
print('imported sourmash:', sourmash, file=sys.stderr)
from sourmash import MinHash
import sourmash.signature

record = next(iter(screed.open(sys.argv[1])))
print('loaded', record.name, file=sys.stderr)

mh = sourmash_lib.MinHash(ksize=K, n=500, is_protein=True)
mh = sourmash.MinHash(ksize=K, n=500, is_protein=True)
prot_ksize = int(K / 3)

for kmer in kmers(record.sequence, prot_ksize):
Expand All @@ -87,5 +87,5 @@ def kmers(seq, k):

mh.add_hash(hash)

s = sourmash_lib.signature.SourmashSignature('', mh, name=record.name)
print(sourmash_lib.signature.save_signatures([s]))
s = sourmash.signature.SourmashSignature('', mh, name=record.name)
print(sourmash.signature.save_signatures([s]))
14 changes: 7 additions & 7 deletions utils/compute-prot-mh-another-way.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,15 +67,15 @@ def kmers(seq, k):

import sys, screed
import mmh3
import sourmash_lib
print('imported sourmash:', sourmash_lib, file=sys.stderr)
from sourmash_lib import MinHash
import sourmash_lib.signature
import sourmash
print('imported sourmash:', sourmash, file=sys.stderr)
from sourmash import MinHash
import sourmash.signature

record = next(iter(screed.open(sys.argv[1])))
print('loaded', record.name, file=sys.stderr)

mh = sourmash_lib.MinHash(ksize=K, n=500, is_protein=True)
mh = sourmash.MinHash(ksize=K, n=500, is_protein=True)
prot_ksize = int(K / 3)

for trans in translate(record.sequence):
Expand All @@ -88,5 +88,5 @@ def kmers(seq, k):

mh.add_hash(hash)

s = sourmash_lib.signature.SourmashSignature('', mh, name=record.name)
print(sourmash_lib.signature.save_signatures([s]))
s = sourmash.signature.SourmashSignature('', mh, name=record.name)
print(sourmash.signature.save_signatures([s]))
37 changes: 0 additions & 37 deletions utils/setname.py
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