add unpassaged sequence files

Previously repo was missing `*.json.gz` files for unpassaged sequences in data, so couldn't run `max_frequency_analysis.ipynb`.
jbloomlab · Jul 23, 2018 · fa06f23 · fa06f23
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diff --git a/analysis_code/.gitignore b/analysis_code/.gitignore
@@ -4,3 +4,4 @@ run.sbatch
 slurm*
 *.pyc
 .ipynb_checkpoints
+!*.json.gz
diff --git a/analysis_code/README.md b/analysis_code/README.md
@@ -23,6 +23,8 @@ The [./data/](./data/) subdirectory contains the following input files:
   * `domains.csv`: csv file listing each site and its associated HA domain
   * `flu_h3n2_ha_1968_2018_6v_frequencies.json.gz`: `JSON` file of the frequency trajectories of all nodes in a human H3N2 phylogeny (see file below)
   * `flu_h3n2_ha_1968_2018_6v_tree.json.gz`: tree build of human H3N2 influenza virus HA sequences from 1968 to 2018 in a `JSON` file format
+  * `flu_h3n2_ha_1968_2018_30v_unpassaged_frequencies.json.gz`: `JSON` file of the frequency trajectories of all nodes in a human H3N2 phylogeny using only unpassaged viruses (see file below)
+  * `flu_h3n2_ha_1968_2018_30v_unpassaged_tree.json.gz`: tree build of only unpassaged human H3N2 influenza virus HA sequences from 1968 to 2018 in a `JSON` file format
   * `H1toH3_renumber.csv`: file to convert from H1 sequential numbering to H3 numbering
   * `H3_human_alignment.fa`: file of subsampled human seasonal H3N2 HA sequences for running `phydms`
   * `H3_swine_alignment.fa`: file of subsampled swine H3N2 HA sequences for running `phydms`

diff --git a/analysis_code/data/flu_h3n2_ha_1968_2018_30v_unpassaged_frequencies.json.gz b/analysis_code/data/flu_h3n2_ha_1968_2018_30v_unpassaged_frequencies.json.gz
diff --git a/analysis_code/data/flu_h3n2_ha_1968_2018_30v_unpassaged_tree.json.gz b/analysis_code/data/flu_h3n2_ha_1968_2018_30v_unpassaged_tree.json.gz