Mercurial > repos > iuc > khmer_filter_abundance

comparison filter-below-abund.py @ 5:a4970dfc331c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 19ea4feff5ccf3744c549b9a67259947a1cb90ba
author iuc
date Sat, 21 Jan 2017 14:43:16 -0500
parents 1ab159863b55
children dbe616d126b1
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4:1ab159863b55 5:a4970dfc331c
32 # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 32 # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
33 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 33 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
34 # 34 #
35 # Contact: khmer-project@idyll.org 35 # Contact: khmer-project@idyll.org
36 from __future__ import print_function 36 from __future__ import print_function
37
38 import os
37 import sys 39 import sys
38 import os 40
39 import khmer 41 import khmer
40 from khmer.thread_utils import ThreadedSequenceProcessor, verbose_fasta_iter 42 from khmer.thread_utils import ThreadedSequenceProcessor, verbose_fasta_iter
41 43
42 WORKER_THREADS = 8 44 WORKER_THREADS = 8
43 GROUPSIZE = 100 45 GROUPSIZE = 100
44
45 CUTOFF = 50 46 CUTOFF = 50
46
47 ###
48 47
49 48
50 def main(): 49 def main():
51 counting_ht = sys.argv[1] 50 counting_ht = sys.argv[1]
52 infiles = sys.argv[2:] 51 infiles = sys.argv[2:]