目录
- datasetscleaned up in repo, made all files mode 7551年前
- Cutoff_Node.pymade kirstines scripts easier to use for workflow (old, I just forgot to add them)2年前
- LICENSECreate LICENSE1年前
- OOP_gfa_parser.pyadded command line support2年前
- README.mdcleaned up in repo, made all files mode 7551年前
- Rotation_and_Orientation.pyadded old scripts2年前
- VG_diterative.pycleaned up in repo, made all files mode 7551年前
- VG_iterative.pymade kirstines scripts easier to use for workflow (old, I just forgot to add them)2年前
- cut_and_rot.pycleaned up in repo, made all files mode 7551年前
- cut_and_rot_orient.pycleaned up in repo, made all files mode 7551年前
- cut_and_rot_rebuild.pycleaned up in repo, made all files mode 7551年前
- example.txtcleaned up in repo, made all files mode 7551年前
- jaccard_dit_wrapper.pyadded shebangs to the other scripts. made subprocess call by script name instead of python3 + path. this makes the wrapper able to handle dynamic paths1年前
- kmer_jaccard.pyadded shebangs to the other scripts. made subprocess call by script name instead of python3 + path. this makes the wrapper able to handle dynamic paths1年前
- kmer_rotation_multiprocessing.pycleaned up in repo, made all files mode 7551年前
- loop_n.shmade noisify rotate to any random point in sequence instead of multiples of 90 degrees. added bash wrapper to iteratively run python wrapper. Bash wrapper loops from 1..n of the inputs of ordered.txt1年前
- meta.yamlcorrection of readme and meta.yaml1年前
- noisify.pycleaned up in repo, made all files mode 7551年前
- offset_fasta.pyadded script that rotates circular fastas2年前
- request_fastas.pycleaned up in repo, made all files mode 7551年前
- run_mars_replicates.shsalvaged run_replicates, fixed_run_mars. It is hard to the bash redirection of mafft outputs with time, so i didn't1年前
- run_replicates.shadded band width to run_rep.sh, not sure what i changed to kmer_jaccard1年前
- test_args.shadded bash script for testing performance of different -m -w values1年前
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STEP 1: Install conda: https://docs.anaconda.com/miniconda/install/#quick-command-line-install STEP 2: conda install -y conda-build conda install -y bioconda-utils conda config –add channels defaults conda config –add channels bioconda conda config –add channels conda-forge STEP 3: conda build meta.yaml STEP 4: conda create -n vgOrient-env vgoreint –use-local conda activate vgOrient-env STEP 5: jaccard_dit_wrapper.py datasets/suina/*.fasta –vg_output_dir VG_OUTPUT_DIR –output OUTPUT_NAME –orientation –min_jaccard_init -w 512 -m 256