In [7]:

    

# Combine the sequences after QC
%run ../scripts/combine_seqs.py --i ../data/mock_community/fasta --type FASTA --output ../data/mock_community/fasta/combined


    

    




../data/mock_community/fasta/SRR072232.fna	SRR072232	839297
../data/mock_community/fasta/SRR072233.fna	SRR072233	576291
../data/mock_community/fasta/SRR172902.fna	SRR172902	2373185
../data/mock_community/fasta/SRR172903.fna	SRR172903	2538639

In [9]:

    

combine_seqs = "../scripts/combine_seqs.py"
# Combine the sequences after QC
%run {combine_seqs} --i ../data/mock_community/subsampled --type FASTA --output ../data/mock_community/subsampled/combined


    

    




../data/mock_community/subsampled/SRR172903.strandex.fna	SRR172903.strandex	500000
../data/mock_community/subsampled/SRR072233.strandex.fna	SRR072233.strandex	500000
../data/mock_community/subsampled/SRR072232.strandex.fna	SRR072232.strandex	500000
../data/mock_community/subsampled/SRR172902.strandex.fna	SRR172902.strandex	500000

In [10]:

    

!shogun --version


    

    




/export/scratch/miniconda3/envs/analysis_SHOGUN/lib/python3.5/site-packages/matplotlib/__init__.py:841: UserWarning: Found matplotlib configuration in ~/.matplotlib/. To conform with the XDG base directory standard, this configuration location has been deprecated on Linux, and the new location is now /home/grad00/hillm096/.config/matplotlib/. Please move your configuration there to ensure that matplotlib will continue to find it in the future.
  _get_xdg_config_dir())
Error: no such option: --version