From a06d66f8171a7fc0ac8e00782c88ed5df50dca82 Mon Sep 17 00:00:00 2001
From: nikos <n.pappas@uu.nl>
Date: Tue, 12 Jan 2021 11:19:04 +0100
Subject: [PATCH] fix tree output formatting
---
README.md | 43 +++++++++++++++++++++++++++----------------
1 file changed, 27 insertions(+), 16 deletions(-)
diff --git a/README.md b/README.md
index 2c5dfad..e510c3a 100644
--- a/README.md
+++ b/README.md
@@ -13,7 +13,8 @@ tou do not need to worry about getting models or any other external databases.
|Tool (source) | Publication/Preprint |
|:------|:------|
-[RaFAh](https://sourceforge.net/projects/rafah/)|[Coutinho F. H. et al. 2020](https://www.biorxiv.org/content/10.1101/2020.09.25.313155v1?rss=1)
+[HTP](https://github.com/wojciech-galan/viruses_classifier)|[Gałan W. et al., 2019](https://www.nature.com/articles/s41598-019-39847-2)
+[RaFAh](https://sourceforge.net/projects/rafah/)|[Coutinho F. H. et al., 2020](https://www.biorxiv.org/content/10.1101/2020.09.25.313155v1?rss=1)
[vHuLK](https://github.com/LaboratorioBioinformatica/vHULK)|[Amgarten D. et al., 2020](https://www.biorxiv.org/content/10.1101/2020.12.06.413476v1)
[VirHostMatcher-Net](https://github.com/WeiliWw/VirHostMatcher-Net)|[Wang W. et al., 2020](https://doi.org/10.1093/nargab/lqaa044])
[WIsH](https://github.com/soedinglab/WIsH)|[Galiez G. et al., 2017](https://academic.oup.com/bioinformatics/article/33/19/3113/3964377)
@@ -36,7 +37,7 @@ The file `environment.txt` can be used to recreate the complete environment
used during development.
> The provided `environment.txt` contains an explicit list of all packages,
-> produced with `conda list -n hp --explicit > environment.txt` .
+> produced with `conda list -n phap --explicit > environment.txt` .
> This ensures all packages are exactly the same versions/builds, so we
> minimize the risk of running into dependencies issues
@@ -158,8 +159,12 @@ For each sample, results for each tool are stored in directories named after
the tool. An example looks like this:
```
-results/A/
+$ tree -L2 results/A
+results/A
├── all_predictions.tsv
+├── htp
+│  ├── predictions.tsv
+│  └── raw.txt
├── rafah
│  ├── A_CDS.faa
│  ├── A_CDS.fna
@@ -183,47 +188,53 @@ results/A/
│  └── results
└── wish
├── llikelihood.matrix
- ├── prediction.list
- └── predictions.tsv
+ ├── prediction.list
+ └── predictions.tsv
```
### Per sample
* `all_predictions.tsv`: Contains the best prediction per contig (rows) for
-each tool along with its confidence/p-value/whatever single value each tool
+each tool along with its confidence/p-value/whatever-single-value each tool
uses to evaluate its confidence in the prediction.
An example for three genomes:
```
-contig vhulk_pred vhulk_score rafah_pred rafah_score vhmnet_pred vhmnet_score wish_pred wish_score
-NC_005964.2 None 4.068828 Mycoplasma 0.461 Mycoplasma fermentans 0.9953 Bacteria;Tenericutes;Mollicutes;Mycoplasmatales;Mycoplasmataceae;Mycoplasma;Mycoplasma fermentans;Mycoplasma fermentans MF-I2 -1.2085700000000001
-NC_015271.1 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 Bacillus 0.0012575098 Bacillus 0.55 Clostridium sp. LS 1.0000 Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium;Clostridium beijerinckii;Clostridium beijerinckii -1.29454
+contig htp_proba vhulk_pred vhulk_score rafah_pred rafah_score vhmnet_pred vhmnet_score wish_pred wish_score
+NC_005964.2 0.8464285626352002 None 4.068828 Mycoplasma 0.461 Mycoplasma fermentans 0.9953 Bacteria;Tenericutes;Mollicutes;Mycoplasmatales;Mycoplasmataceae;Mycoplasma;Mycoplasma fermentans;Mycoplasma fermentans MF-I2 -1.2085700000000001
+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
```
* `tmp` directory
- * Contains one fasta file per input genome, along with other intermediate
-files necessary for a smooth execution of the workflow.
+ * 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)
### Per tool
+* `htp`
+ * 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.
+
* `rafah`
- * All files prefixed with `<sample_id>_` are the rafah's raw output
+ * 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`
* `vhulk`
- * `results.csv`: Copy of the `results/sample/tmp/genomes/results/results.csv`
- * `predictions.tsv`: A selection of the 1st (`BIN/genome`), 10th (`final_prediction`)
+ * 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`.
* `vhmnet`
* Directories `feature_values` and `predictions` are the raw output
* Directory `tmp` is a temporary dir written by `VirHostMatcher-Net` for
doing its magic.
- * `predictions.tsv` contain contig, host taxonomy and scores.
+ * File `predictions.tsv` contains contig, host taxonomy and scores.
* `wish`
* Files `llikelihood.matrix` and `prediction.list` are the raw output
--
GitLab