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**/.DS_Store
**/.ipynb_checkpoints
**/__pycache__
src/generated/pubchem_dicts/inchikey_to_pubchem.pickle
src/generated/metanetx_4_4/chem_xref.tsv
src/generated/metanetx_4_4/chem_prop.tsv
src/generated/metanetx_4_4/reac_xref.tsv
src/generated/pubchem/pc_inchikey2compound_000004.ttl
src/generated/pubchem/pc_inchikey2compound_000001.ttl
src/generated/pubchem/pc_inchikey2compound_000010.ttl
src/generated/pubchem/pc_inchikey2compound_000008.ttl
src/generated/pubchem/pc_inchikey2compound_000006.ttl
src/generated/pubchem/pc_inchikey2compound_000007.ttl
src/generated/pubchem/pc_inchikey2compound_000009.ttl
src/generated/pubchem/pc_inchikey2compound_000002.ttl
src/generated/pubchem/pc_inchikey2compound_000005.ttl
src/generated/pubchem/pc_inchikey2compound_000003.ttl
src/generated/mnx_dicts_M/smiles.pickle
src/generated/mnx_dicts_M/inchi.pickle
src/generated/mnx_dicts_M/inchikey.pickle
src/generated/mnx_dicts_M/crossrefs.pickle
validation/01_klebsiella/validation/gempipe/working/rec_broken/sequences.csv
validation/01_klebsiella/validation/gempipe/working/rec_masking/sequences.csv
validation/01_klebsiella/validation/gempipe/working/clustering/sequences.csv
validation/01_klebsiella/validation/gempipe/working/clustering/combined.faa
validation/01_klebsiella/validation/gempipe/working/rec_overlap/sequences.csv
validation/gapseq_v1.3.1/dat/seq/Bacteria/unrev/sequences.tar.gz
validation/gapseq_v1.3.1/dat/seq/Bacteria/unrev/7ccc5cd23660f087629258dec00384ef.fasta
validation/gapseq_v1.3.1/dat/seq/Bacteria/unrev/d8f4388392492f58e09fd15edab321af.fasta
validation/03_pseudomonas/validation/gempipe_tcdb/working/rec_broken/sequences.csv
validation/03_pseudomonas/validation/gempipe_tcdb/working/rec_masking/sequences.csv
validation/03_pseudomonas/validation/gempipe_tcdb/working/clustering/sequences.csv
validation/03_pseudomonas/validation/gempipe_tcdb/working/clustering/combined.faa
validation/03_pseudomonas/validation/gempipe_tcdb/working/rec_overlap/sequences.csv
validation/03_pseudomonas/validation/gempipe/working/rec_broken/sequences.csv
validation/03_pseudomonas/validation/gempipe/working/rec_masking/sequences.csv
validation/03_pseudomonas/validation/gempipe/working/clustering/sequences.csv
validation/03_pseudomonas/validation/gempipe/working/clustering/combined.faa
validation/03_pseudomonas/validation/gempipe/working/rec_overlap/sequences.csv
validation/dbs/eggnog_proteins.dmnd
validation/dbs/eggnog.taxa.db
validation/dbs/eggnog.db
testing/09_aphidicola_auto2/working/dbs/eggnog_proteins.dmnd
testing/09_aphidicola_auto2/working/dbs/eggnog.taxa.db
testing/09_aphidicola_auto2/working/dbs/eggnog.db
applications/plantarum/old_stuff/pa_matrix_refound_frag.csv
applications/plantarum/gempipe/working/coordinates/seq_to_coords.pickle
applications/plantarum/gempipe/working/rec_broken/pam.csv
applications/plantarum/gempipe/working/rec_broken/seq_to_coords.pickle
applications/plantarum/gempipe/working/rec_broken/sequences.csv
applications/plantarum/gempipe/working/rec_masking/pam.csv
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applications/plantarum/gempipe/working/rec_masking/sequences.csv
applications/plantarum/gempipe/working/clustering/representatives.faa.clstr
applications/plantarum/gempipe/working/clustering/pam.csv
applications/plantarum/gempipe/working/clustering/acc_to_seqs.pickle
applications/plantarum/gempipe/working/clustering/seq_to_cluster.pickle
applications/plantarum/gempipe/working/clustering/cluster_to_seqs.pickle
applications/plantarum/gempipe/working/clustering/sequences.csv
applications/plantarum/gempipe/working/clustering/combined.faa
applications/plantarum/gempipe/working/clustering/seq_to_acc.pickle
applications/plantarum/gempipe/working/rec_overlap/pam.csv
applications/plantarum/gempipe/working/rec_overlap/seq_to_coords.pickle
applications/plantarum/gempipe/working/rec_overlap/sequences.csv
applications/plantarum/gempipe/output_recon/pam.csv
applications/limosilactobacillus_reuteri/fastani/ANIclustermap.svg
applications/limosilactobacillus_reuteri/gempipe/working/coordinates/seq_to_coords.pickle
applications/limosilactobacillus_reuteri/gempipe/working/rec_broken/seq_to_coords.pickle
applications/limosilactobacillus_reuteri/gempipe/working/rec_broken/sequences.csv
applications/limosilactobacillus_reuteri/gempipe/working/rec_masking/seq_to_coords.pickle
applications/limosilactobacillus_reuteri/gempipe/working/rec_masking/sequences.csv
applications/limosilactobacillus_reuteri/gempipe/working/clustering/sequences.csv
applications/limosilactobacillus_reuteri/gempipe/working/clustering/combined.faa
applications/limosilactobacillus_reuteri/gempipe/working/rec_overlap/seq_to_coords.pickle
applications/limosilactobacillus_reuteri/gempipe/working/rec_overlap/sequences.csv
applications/lacticaseibacillus/gempipe/working/coordinates/seq_to_coords.pickle
applications/lacticaseibacillus/gempipe/working/rec_broken/pam.csv
applications/lacticaseibacillus/gempipe/working/rec_broken/seq_to_coords.pickle
applications/lacticaseibacillus/gempipe/working/rec_broken/sequences.csv
applications/lacticaseibacillus/gempipe/working/rec_masking/pam.csv
applications/lacticaseibacillus/gempipe/working/rec_masking/seq_to_coords.pickle
applications/lacticaseibacillus/gempipe/working/rec_masking/sequences.csv
applications/lacticaseibacillus/gempipe/working/clustering/representatives.faa.clstr
applications/lacticaseibacillus/gempipe/working/clustering/pam.csv
applications/lacticaseibacillus/gempipe/working/clustering/acc_to_seqs.pickle
applications/lacticaseibacillus/gempipe/working/clustering/seq_to_cluster.pickle
applications/lacticaseibacillus/gempipe/working/clustering/cluster_to_seqs.pickle
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