From 2bc55e4df5bf793f53a5e91470e188efdd6d9268 Mon Sep 17 00:00:00 2001
From: papanikos <n.pappas@uu.nl>
Date: Fri, 15 Jan 2021 09:27:47 +0100
Subject: [PATCH] extend dropdowns
---
README.md | 38 ++++++++++++++++++++++++++++----------
1 file changed, 28 insertions(+), 10 deletions(-)
diff --git a/README.md b/README.md
index 48c24ae..a290369 100644
--- a/README.md
+++ b/README.md
@@ -224,10 +224,12 @@ results/A
└── predictions.tsv
```
-<details>
-<summary>Per sample</summary>
+###Per sample
+---
-* `all_predictions.tsv`: Contains the best prediction per contig (rows) for
+<details>
+<summary>`all_predictions.tsv`</summary>
+Contains the best prediction per contig (rows) for
each tool along with its confidence/p-value/whatever-single-value each tool
uses to evaluate its confidence in the prediction.
@@ -239,8 +241,11 @@ NC_005964.2 0.8464285626352002 None 4.068828 Mycoplasma
NC_015271.1 0.995161392517451 Escherichia_coli 1.0301523 Salmonella 0.495 Muricauda pacifica 0.9968 Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Raoultella;Raoultella sp. NCTC 9187;Raoultella sp. NCTC 9187 -1.3869200000000002
NC_023719.1 0.9999957241187084 Bacillus 0.0012575098 Bacillus 0.55 Clostridium sp. LS 1.0000 Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium;Clostridium beijerinckii;Clostridium beijerinckii -1.29454
```
+</details>
-* File `lca.tsv`: Last Common Ancestor of predictions, based on taxonomy
+<details>
+<summary>`lca.tsv`</summary>
+Last Common Ancestor of predictions, based on taxonomy
An example for the genomes above:
```
@@ -249,8 +254,10 @@ NC_005964.2 Mycoplasma genus 2093
NC_015271.1 Enterobacteriaceae family 543
NC_023719.1 Firmicutes phylum 1239
```
+</details>
-* `tmp` directory
+<details>
+<summary>`tmp` (dir)</summary>
* Directory `genomes`: Contains one fasta file per input genome
* File `reflist.txt`: An intermediate file that holds paths to all produced
genome fastas (used as intermediate file to ensure smooth execution)
@@ -259,36 +266,47 @@ genome fastas (used as intermediate file to ensure smooth execution)
### Per tool
-* `htp`
+<details>
+<summary>`htp`</summary>
* File `raw.txt`: The raw output of `htp` per contig
* File `predictions.tsv`: **Two**-column separated tsv with contig id and
probability of host being a phage.
+</details>
-* `rafah`
+<details>
+<summary>`rafah`</summary>
* Files prefixed with `<sample_id>_` are the rafah's raw output
* `predictions.tsv`: A selection of the 1st (`Contig`) , 6th
(`Predicted_Host`) and 7th (`Predicted_Host_Score`) columns from file
`<sample_id>_Seq_Info.tsv`
+</details>
-* `vhulk`
+<details>
+<summary>`vhulk`</summary>
* File `results.csv`: Copy of the `results/sample/tmp/genomes/results/results.csv`
* File `predictions.tsv`: A selection of the 1st (`BIN/genome`), 10th (`final_prediction`)
11th (`entropy`) columns from file `results.csv`.
+</details>
-* `vhmnet`
+<details>
+<summary>`vhmnet`</summary>
* Directories `feature_values` and `predictions` are the raw output
* Directory `tmp` is a temporary dir written by `VirHostMatcher-Net` for
doing its magic.
* File `predictions.tsv` contains contig, host taxonomy and scores.
+</details>
-* `wish`
+<details>
+<summary>`wish`</summary>
* Files `llikelihood.matrix` and `prediction.list` are the raw output
* File `predictions.tsv` has contig, host taxonomy and **llikelihood** scores.
+</details>
+
### Logs
--
GitLab