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a/figure6/de_replicated_faas/NODE_9_length_80003_cov_6.779119.faa b/figure6/data_files/de_replicated_faas/NODE_9_length_80003_cov_6.779119.faa similarity index 100% rename from figure6/de_replicated_faas/NODE_9_length_80003_cov_6.779119.faa rename to figure6/data_files/de_replicated_faas/NODE_9_length_80003_cov_6.779119.faa diff --git a/figure6/de_replicated_fnas.csv b/figure6/data_files/de_replicated_fnas.csv similarity index 100% rename from figure6/de_replicated_fnas.csv rename to figure6/data_files/de_replicated_fnas.csv diff --git a/figure6/dereplicated_mmseqs_faa_cluster.tsv b/figure6/data_files/dereplicated_mmseqs_faa_cluster.tsv similarity index 100% rename from figure6/dereplicated_mmseqs_faa_cluster.tsv rename to figure6/data_files/dereplicated_mmseqs_faa_cluster.tsv diff --git a/figure6/mcp.faa b/figure6/data_files/mcp.faa similarity index 100% rename from figure6/mcp.faa rename to figure6/data_files/mcp.faa diff --git a/figure6/mcp_contigs.fna b/figure6/data_files/mcp_contigs.fna similarity index 100% rename from figure6/mcp_contigs.fna rename to figure6/data_files/mcp_contigs.fna diff --git a/figure6/figure_6b.ipynb b/figure6/figure_6b.ipynb index 3582fdf..a5fe8a3 100644 --- a/figure6/figure_6b.ipynb +++ b/figure6/figure_6b.ipynb @@ -55,7 +55,7 @@ "metadata": {}, "outputs": [], "source": [ - "cluster_tsv = pd.read_csv('dereplicated_mmseqs_faa_cluster.tsv', sep='\\t', header=None)\n", + "cluster_tsv = pd.read_csv('data_files/dereplicated_mmseqs_faa_cluster.tsv', sep='\\t', header=None)\n", "cluster_tsv.columns = ['cluster_id', 'protein_id']" ] }, @@ -86,7 +86,7 @@ "metadata": {}, "outputs": [], "source": [ - "contig_dir = 'de_replicated_faas/'\n", + "contig_dir = 'data_files/de_replicated_faas/'\n", "contigs = os.listdir(contig_dir)" ] }, @@ -127,7 +127,7 @@ "metadata": {}, "outputs": [], "source": [ - "capsid_ids, _ = get_faa('mcp.faa')\n", + "capsid_ids, _ = get_faa('data_files/mcp.faa')\n", "capsid_ids = [i.split(' ')[0][1:] for i in capsid_ids]\n", "capsid_clusters = set([p_c[i] for i in capsid_ids if i in p_c])\n", "\n", @@ -154,7 +154,7 @@ "metadata": {}, "outputs": [], "source": [ - "cluster_predictions = pd.read_csv('cluster_predicted_PHROG_category.csv')" + "cluster_predictions = pd.read_csv('data_files/cluster_predicted_PHROG_category.csv')" ] }, { @@ -286,14 +286,6 @@ "## output graph for cytoscape visualization\n", "nx.write_graphml(G, 'network.graphml')" ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "8d8a514b", - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": {