From messyasa at oregonstate.edu  Tue Jan 30 13:05:34 2018
From: messyasa at oregonstate.edu (Messyasz, Adriana)
Date: Tue, 30 Jan 2018 13:05:34 -0800
Subject: [khmer] khmer/sandbox filter-below-abund.py script error
Message-ID: <CAEOfy1PLQsOyYp_jcA85=H49FSdMa02L61eOvKvpSKS0j1aBXg@mail.gmail.com>

Hello,

I am trying to run the khmer/sandbox/filter-below-abund.py script in order
to trim off high-abundance kmers for a metagenome assembly.

Below is the command I want to run:
python /local/cluster/khmer-legacy/sandbox/filter-below-abund.py
4B_hostfilt_count
4B_norm_hostfilt.fq --cutoff 50 -T 5 -M 100

The 4B_hostfilt_count file is the countgraph file created via
load-into-counting.py and the 4B_norm_hostfilt.fq file is sequence file
after normalization (normalize-by-median.py).

And this is the error I receive:

Traceback (most recent call last):

  File "/local/cluster/khmer-legacy/sandbox/filter-below-abund.py", line
49, in <module>

    main()

  File "/local/cluster/khmer-legacy/sandbox/filter-below-abund.py", line
22, in main

    ht = khmer.load_counting_hash(counting_ht)

AttributeError: 'module' object has no attribute 'load_counting_hash'

I am concerned that I am getting this error because the
filter-below-abund.py script is no longer part of the khmer pipeline.

The newest installed khmer in our linux /local/cluster/bin is version
2.0+103.g8300de0,
but the filter-below-abundance.py script did not show up after the
installation.

The script I used came from an older installation of khmer in
/local/cluster.

(The python version I am using: Python 2.7.14, and the OS Version:
Linux 3.10.0-693.11.6.el7.x86_64 x86_64)

I wanted to know if anyone would know why I am getting this error, if the
filter-below-abund.py script should be included in installations of the
latest khmer version, and if this script is still functioning.

Thank you,
Adriana Messyasz

-- 
Adriana Messyasz
<http://vegathurberlab.oregonstate.edu/people/adriana-messyasz>
Ph.D. Student
Vega Thurber Lab
Oregon State University
Corvallis, OR 97331
email: messyasa at oregonstate.edu
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