diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index e69f75d..7a496dd 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -19,4 +19,4 @@
]
}
}
-}
\ No newline at end of file
+}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 133e214..038a803 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -3,7 +3,6 @@ name: ci
on:
push:
-
jobs:
test:
runs-on: ubuntu-latest
diff --git a/INSTALLATION.md b/INSTALLATION.md
index 37c6135..0b0c57c 100644
--- a/INSTALLATION.md
+++ b/INSTALLATION.md
@@ -19,9 +19,9 @@ To install Whiscy, follow these steps:
- Clone the repository:
- ```bash
- git clone https://github.com/haddocking/whiscy && cd whiscy
- ```
+ ```bash
+ git clone https://github.com/haddocking/whiscy && cd whiscy
+ ```
- Install the scripts
@@ -33,23 +33,23 @@ To install Whiscy, follow these steps:
- Check the installation
- ```text
- $ whiscy -h
- usage: whiscy [-h] [-o output_file] [--version]
- surface_list conversion_table alignment_file distance_file
-
- positional arguments:
- surface_list Surface list
- conversion_table Conversion table
- alignment_file Alignment file
- distance_file Distance file
-
- options:
- -h, --help show this help message and exit
- -o output_file, --output output_file
- If set, output prediction to this file
- --version show program's version number and exit
- ```
+ ```text
+ $ whiscy -h
+ usage: whiscy [-h] [-o output_file] [--version]
+ surface_list conversion_table alignment_file distance_file
+
+ positional arguments:
+ surface_list Surface list
+ conversion_table Conversion table
+ alignment_file Alignment file
+ distance_file Distance file
+
+ options:
+ -h, --help show this help message and exit
+ -o output_file, --output output_file
+ If set, output prediction to this file
+ --version show program's version number and exit
+ ```
### Troubleshooting
diff --git a/USAGE.md b/USAGE.md
index 5aa75af..d36783f 100644
--- a/USAGE.md
+++ b/USAGE.md
@@ -10,9 +10,9 @@ Below we will give an example of how to use WHISCY to predict the binding site o
Download the PDB file of the protein 1PPE from the [RCSB PDB](https://www.rcsb.org/structure/1PPE) website.
- ```bash
- wget https://files.rcsb.org/download/1PPE.pdb
- ```
+```bash
+wget https://files.rcsb.org/download/1PPE.pdb
+```
### Setup the prediction
@@ -32,26 +32,26 @@ $ whiscy_setup 1PPE.pdb E
2024-04-22 11:44:44,046 cli_setup:319 INFO - Protdist calculated
2024-04-22 11:44:44,054 cli_setup:326 INFO - Conversion table file generated
2024-04-22 11:44:44,054 cli_setup:328 INFO - Whiscy setup finished
- ```
+```
This script will generate a set of files needed for the prediction step with `whiscy`. Here it is a list of the generated files in our 1PPE complex.
> Follow the links to see a set of pre-generated files for the 1PPE protein.
-| File name | Explanation |
-| ----------------------------------------- |----------------------------------------------------------------|
-| [1ppe.hssp](example/1ppe.hssp) | Multiple sequence alignment download from the HSSP database |
-| [1ppe.hssp.bz2](example/1ppe.hssp.bz2) | HSSP MSA file compressed |
-| [1ppe.pdb](example/1ppe.pdb) | PDB file download from the Protein Data Bank |
-| [1ppe_E.pdb](example/1ppe_E.pdb) | 1ppe.pdb parsed to select only the given `chain_id` |
-| [1ppe_E.rsa](example/1ppe_E.rsa) | SASA output of `freesasa` in `NACCESS` format of `1ppe_E.pdb` file|
-| [1ppe_E.fasta](example/1ppe_E.fasta) | Sequence of 1ppe_E.pdb. Alternative residues have been removed |
-| [1ppe_E.phylseq](example/1ppe_E.phylseq) | MSA file translated from HSSP to PHYLIP format |
-| [1ppe_E.conv](example/1ppe_E.conv) | PDB residue numeration to FASTA sequence numeration |
-| [1ppe_E.out](example/1ppe_E.out) | Output of the `protdist` software on 1ppe_E.pdb |
-| [1ppe_E.sur](example/1ppe_E.sur) | >15 % surface residue list according to `sa_pred_cutoff` cutoff |
-| [1ppe_E.suract](example/1ppe_E.suract) | >40 % surface residue list according to `sa_act_cutoff` cutoff |
-| [1ppe_E.lac](example/1ppe_E.lac) | 0-15 % accessible residue list |
+| File name | Explanation |
+| ---------------------------------------- | ------------------------------------------------------------------ |
+| [1ppe.hssp](example/1ppe.hssp) | Multiple sequence alignment download from the HSSP database |
+| [1ppe.hssp.bz2](example/1ppe.hssp.bz2) | HSSP MSA file compressed |
+| [1ppe.pdb](example/1ppe.pdb) | PDB file download from the Protein Data Bank |
+| [1ppe_E.pdb](example/1ppe_E.pdb) | 1ppe.pdb parsed to select only the given `chain_id` |
+| [1ppe_E.rsa](example/1ppe_E.rsa) | SASA output of `freesasa` in `NACCESS` format of `1ppe_E.pdb` file |
+| [1ppe_E.fasta](example/1ppe_E.fasta) | Sequence of 1ppe_E.pdb. Alternative residues have been removed |
+| [1ppe_E.phylseq](example/1ppe_E.phylseq) | MSA file translated from HSSP to PHYLIP format |
+| [1ppe_E.conv](example/1ppe_E.conv) | PDB residue numeration to FASTA sequence numeration |
+| [1ppe_E.out](example/1ppe_E.out) | Output of the `protdist` software on 1ppe_E.pdb |
+| [1ppe_E.sur](example/1ppe_E.sur) | >15 % surface residue list according to `sa_pred_cutoff` cutoff |
+| [1ppe_E.suract](example/1ppe_E.suract) | >40 % surface residue list according to `sa_act_cutoff` cutoff |
+| [1ppe_E.lac](example/1ppe_E.lac) | 0-15 % accessible residue list |
### Make the interface prediction
diff --git a/media/1ppe_whiscy.png b/media/1ppe_whiscy.png
index be94248..32f8b8c 100644
Binary files a/media/1ppe_whiscy.png and b/media/1ppe_whiscy.png differ
diff --git a/media/loch_haddock.png b/media/loch_haddock.png
index 270547a..124f6b1 100644
Binary files a/media/loch_haddock.png and b/media/loch_haddock.png differ
diff --git a/media/whiscy_logo.png b/media/whiscy_logo.png
index 858c191..b872b8c 100644
Binary files a/media/whiscy_logo.png and b/media/whiscy_logo.png differ
diff --git a/media/whiscy_logo.svg b/media/whiscy_logo.svg
index 7692ee7..24c0894 100644
--- a/media/whiscy_logo.svg
+++ b/media/whiscy_logo.svg
@@ -1,125 +1 @@
-
-
+
\ No newline at end of file
diff --git a/src/whiscy/cli_consadjust.py b/src/whiscy/cli_consadjust.py
index 21706e5..6df7817 100755
--- a/src/whiscy/cli_consadjust.py
+++ b/src/whiscy/cli_consadjust.py
@@ -84,7 +84,7 @@ def main():
neg = True
index = np.argmax(z_values < currz)
- upperz = z_values[index]
+ z_values[index]
if index >= 24999:
pscore = 0.5
diff --git a/src/whiscy/cli_setup.py b/src/whiscy/cli_setup.py
index 5d0bf9c..d49046a 100755
--- a/src/whiscy/cli_setup.py
+++ b/src/whiscy/cli_setup.py
@@ -226,7 +226,7 @@ def main():
hssp_file = hssp_file.replace("hssp", "hssp3")
hssp.decompress_bz2(compressed_hssp_file, hssp_file)
logger.info("HSSP alignment stored to {0}".format(hssp_file))
- except Exception as err:
+ except Exception:
logger.warning("HSSP file could not be downloaded")
try:
if "hssp3" in hssp_file:
diff --git a/src/whiscy/modules/pam_data.py b/src/whiscy/modules/pam_data.py
index 61ec698..6cf97a7 100644
--- a/src/whiscy/modules/pam_data.py
+++ b/src/whiscy/modules/pam_data.py
@@ -1,208 +1,1171 @@
"""Data used in the PAM calc module"""
+code = [
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ 0,
+ -1,
+ 4,
+ 3,
+ 6,
+ 13,
+ 7,
+ 8,
+ 9,
+ -1,
+ 11,
+ 10,
+ 12,
+ 2,
+ -1,
+ 14,
+ 5,
+ 1,
+ 15,
+ 16,
+ -1,
+ 19,
+ 17,
+ -1,
+ 18,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ 0,
+ -1,
+ 4,
+ 3,
+ 6,
+ 13,
+ 7,
+ 8,
+ 9,
+ -1,
+ 11,
+ 10,
+ 12,
+ 2,
+ -1,
+ 14,
+ 5,
+ 1,
+ 15,
+ 16,
+ -1,
+ 19,
+ 17,
+ -1,
+ 18,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+ -1,
+]
-code = [-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, -1,
- 4, 3, 6, 13, 7, 8, 9, -1, 11, 10, 12, 2, -1, 14, 5, 1, 15, 16, -1, 19,
- 17, -1, 18, -1, -1, -1, -1, -1, -1, -1, 0, -1, 4, 3, 6, 13, 7, 8, 9,
- -1, 11, 10, 12, 2, -1, 14, 5, 1, 15, 16, -1, 19, 17, -1, 18, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1]
+logpameigval = [
+ -0.022091252,
+ -0.019297602,
+ 0.000004760,
+ -0.017477817,
+ -0.016575549,
+ -0.015504543,
+ -0.002112213,
+ -0.002685727,
+ -0.002976402,
+ -0.013440755,
+ -0.012926992,
+ -0.004293227,
+ -0.005356688,
+ -0.011064786,
+ -0.010480731,
+ -0.008760449,
+ -0.007142318,
+ -0.007381851,
+ -0.007806557,
+ -0.008127024,
+]
-logpameigval = [-0.022091252,-0.019297602, 0.000004760,-0.017477817,
- -0.016575549,-0.015504543,-0.002112213,-0.002685727,
- -0.002976402,-0.013440755,-0.012926992,-0.004293227,
- -0.005356688,-0.011064786,-0.010480731,-0.008760449,
- -0.007142318,-0.007381851,-0.007806557,-0.008127024]
+pameigvec = [
+ [
+ -0.173697,
+ -0.885673,
+ -1.0049,
+ 0.286697,
+ 1.88382,
+ 1.83495,
+ -0.198369,
+ 0.197182,
+ -0.328623,
+ 0.46536,
+ -0.29925,
+ -0.0965166,
+ -0.74739,
+ -0.854738,
+ 0.678401,
+ -0.183266,
+ 0.192614,
+ -0.482818,
+ 0.146535,
+ 0.0798611,
+ ],
+ [
+ -0.184354,
+ -0.175916,
+ -1.0076,
+ -0.142763,
+ -0.0628839,
+ 0.0139009,
+ 0.141204,
+ 0.331822,
+ -0.539164,
+ -0.708375,
+ 0.0817457,
+ -0.37228,
+ 2.4085,
+ -2.80149,
+ -2.21178,
+ 1.28384,
+ 1.42798,
+ 0.0188545,
+ -0.4161,
+ -0.332652,
+ ],
+ [
+ -3.40863,
+ -0.900981,
+ -0.994619,
+ 2.41327,
+ -0.811826,
+ -0.630945,
+ -0.174313,
+ 0.293746,
+ -0.383093,
+ -1.26984,
+ 0.89058,
+ -0.481288,
+ 0.12826,
+ 0.0590369,
+ 0.799897,
+ -0.296714,
+ -0.552095,
+ 0.384358,
+ 0.177192,
+ 0.169113,
+ ],
+ [
+ 2.46339,
+ -1.69023,
+ -0.992457,
+ 0.277099,
+ -0.415795,
+ -0.0669855,
+ -0.230705,
+ 0.389199,
+ -0.543538,
+ -1.76778,
+ 0.892756,
+ -0.58089,
+ -0.185477,
+ -0.168277,
+ -0.685745,
+ -1.4301,
+ -1.48203,
+ 0.838871,
+ 0.35372,
+ 0.654423,
+ ],
+ [
+ -0.0653222,
+ -0.142554,
+ -1.00875,
+ -0.0956775,
+ 0.00982116,
+ 0.0114652,
+ -0.267974,
+ -5.26286,
+ -1.24758,
+ 0.00651089,
+ -0.0117717,
+ 0.384433,
+ 0.233031,
+ 0.151659,
+ -0.112617,
+ -0.07216,
+ -0.130136,
+ 0.277631,
+ -0.271657,
+ 0.0955676,
+ ],
+ [
+ 0.411745,
+ -1.0016,
+ -0.993702,
+ 1.55374,
+ -0.744468,
+ -0.843633,
+ -0.175287,
+ 0.385097,
+ -0.406764,
+ 3.44619,
+ -1.97631,
+ -0.351715,
+ 0.735297,
+ 0.188087,
+ -0.904437,
+ 0.289089,
+ -1.65422,
+ 0.177167,
+ -0.146884,
+ 0.250162,
+ ],
+ [
+ -1.46727,
+ 2.10777,
+ -0.9997,
+ -1.83253,
+ 0.527169,
+ 0.327848,
+ -0.228532,
+ 0.39569,
+ -0.510345,
+ 0.172614,
+ -0.202514,
+ -0.508889,
+ -0.0845795,
+ -0.16422,
+ -1.27133,
+ -1.46079,
+ -1.68406,
+ 0.685183,
+ 0.331996,
+ 0.684302,
+ ],
+ [
+ -0.0358926,
+ -0.101557,
+ -1.0116,
+ -0.332503,
+ -0.196083,
+ -0.33719,
+ -0.250326,
+ 0.316732,
+ -0.566645,
+ 0.055228,
+ -0.0474809,
+ -0.496718,
+ -1.85709,
+ 0.644994,
+ -0.657107,
+ 0.980698,
+ 0.993692,
+ 1.38279,
+ -0.619067,
+ -0.747332,
+ ],
+ [
+ 0.418693,
+ 0.437099,
+ -0.995008,
+ -0.951753,
+ 0.506729,
+ 0.416234,
+ -0.116331,
+ 0.255448,
+ -0.181811,
+ -0.851382,
+ 0.440693,
+ -0.67166,
+ 1.20247,
+ 0.832078,
+ 1.74873,
+ 3.77201,
+ -2.59574,
+ -0.020501,
+ -0.294246,
+ -0.0926676,
+ ],
+ [
+ 0.125546,
+ -0.0372708,
+ -0.995249,
+ 0.281829,
+ 2.9408,
+ -3.14634,
+ -0.100311,
+ 0.0550663,
+ 0.61025,
+ -0.178163,
+ 0.40751,
+ 1.30446,
+ -0.137214,
+ 0.576156,
+ -0.721845,
+ 0.624154,
+ 0.424991,
+ -0.423803,
+ 1.73362,
+ 1.19383,
+ ],
+ [
+ 0.0180848,
+ 0.0195127,
+ -0.986272,
+ -0.0422427,
+ -0.0639326,
+ 0.0913046,
+ -0.0163454,
+ 0.163283,
+ 1.15374,
+ 0.263141,
+ 0.678789,
+ 2.26955,
+ 0.201714,
+ -0.32496,
+ 0.14775,
+ -0.423257,
+ -0.587479,
+ 0.62248,
+ -1.06261,
+ -1.22256,
+ ],
+ [
+ 0.254528,
+ 0.0789705,
+ -1.00771,
+ -0.252216,
+ 0.231033,
+ 0.338253,
+ -0.122814,
+ 0.41346,
+ -0.510865,
+ 0.460223,
+ 0.425877,
+ -0.347116,
+ 1.89864,
+ 1.78614,
+ 0.739422,
+ -0.88218,
+ 1.38203,
+ 0.548471,
+ 0.111328,
+ -0.142583,
+ ],
+ [
+ -0.106978,
+ -0.00225986,
+ -1.01125,
+ 0.0638037,
+ -0.139527,
+ 0.163789,
+ -0.0895913,
+ 0.233315,
+ 0.587038,
+ -3.85451,
+ -6.80573,
+ 1.53798,
+ 0.593227,
+ 1.02989,
+ 0.45206,
+ -0.415565,
+ 0.350157,
+ 0.343607,
+ 0.0730036,
+ -0.369488,
+ ],
+ [
+ -0.0168964,
+ -0.0313974,
+ -0.978517,
+ -0.0355775,
+ -0.186282,
+ 0.218407,
+ 0.470191,
+ -0.473411,
+ 2.96084,
+ 0.0480287,
+ -0.0359644,
+ -1.19118,
+ -0.103219,
+ 0.0888554,
+ 0.0569158,
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diff --git a/src/whiscy/modules/quotes.py b/src/whiscy/modules/quotes.py
index 901da20..c7fd3ab 100644
--- a/src/whiscy/modules/quotes.py
+++ b/src/whiscy/modules/quotes.py
@@ -1,22 +1,23 @@
import random
-_quotes = {"Mark Twain": "Too much of anything is bad, but too much good whiskey is barely enough.",
- "Raymond Chandler": "There is no bad whiskey. There are only some whiskeys that aren’t as good as others.",
- "Winston Churchill": "The water was not fit to drink. To make it palatable, we had to add whisky. By diligent effort, I learned to like it.",
- "Tommy Cooper": "I’m on a whisky diet. I’ve lost three days already.",
- "Humphrey Bogart": "I should never have switched from Scotch to Martinis.",
- "Johnny Carson": "Happiness is having a rare steak, a bottle of whisky, and a dog to eat the rare steak.",
- "Abraham Lincoln": "Tell me what brand of whiskey that Grant drinks. I would like to send a barrel of it to my other generals.",
- "Alexander Fleming": "A good gulp of hot whiskey at bedtime—it’s not very scientific, but it helps.",
- "W.C. Fields": "Always carry a flagon of whiskey in case of snakebite and furthermore always carry a small snake.",
- "James Joyce": "The light music of whiskey falling into a glass—an agreeable interlude.",
- "Igor Stravinsky": "My God, so much I like to drink Scotch that sometimes I think my name is Igor Stra-whiskey.",
- "Haruki Murakami": "The second whiskey is always my favorite. From the third on, it no longer has any taste. It's just something to pour into your stomach.",
- "Mikael Trellet": "Whiscy, to use without moderation.",
- "Jorge Roel": "Coffee keeps me going until it's acceptable to drink Whiskey"
- }
+_quotes = {
+ "Mark Twain": "Too much of anything is bad, but too much good whiskey is barely enough.",
+ "Raymond Chandler": "There is no bad whiskey. There are only some whiskeys that aren’t as good as others.",
+ "Winston Churchill": "The water was not fit to drink. To make it palatable, we had to add whisky. By diligent effort, I learned to like it.",
+ "Tommy Cooper": "I’m on a whisky diet. I’ve lost three days already.",
+ "Humphrey Bogart": "I should never have switched from Scotch to Martinis.",
+ "Johnny Carson": "Happiness is having a rare steak, a bottle of whisky, and a dog to eat the rare steak.",
+ "Abraham Lincoln": "Tell me what brand of whiskey that Grant drinks. I would like to send a barrel of it to my other generals.",
+ "Alexander Fleming": "A good gulp of hot whiskey at bedtime—it’s not very scientific, but it helps.",
+ "W.C. Fields": "Always carry a flagon of whiskey in case of snakebite and furthermore always carry a small snake.",
+ "James Joyce": "The light music of whiskey falling into a glass—an agreeable interlude.",
+ "Igor Stravinsky": "My God, so much I like to drink Scotch that sometimes I think my name is Igor Stra-whiskey.",
+ "Haruki Murakami": "The second whiskey is always my favorite. From the third on, it no longer has any taste. It's just something to pour into your stomach.",
+ "Mikael Trellet": "Whiscy, to use without moderation.",
+ "Jorge Roel": "Coffee keeps me going until it's acceptable to drink Whiskey",
+}
def get_one():
one = random.choice(list(_quotes))
- return "\"{}\"\n - {}".format(_quotes[one], one)
+ return '"{}"\n - {}'.format(_quotes[one], one)
diff --git a/tests/gold/run_parasmooth.sh b/tests/gold/run_parasmooth.sh
index 924dcb3..3895352 100755
--- a/tests/gold/run_parasmooth.sh
+++ b/tests/gold/run_parasmooth.sh
@@ -1,3 +1,3 @@
#!/bin/bash
-./parasmooth 2SNIE.acons 2SNIE.lcons 2SNIE.rd parasmooth.par > 2SNIE.parasmooth
+./parasmooth 2SNIE.acons 2SNIE.lcons 2SNIE.rd parasmooth.par >2SNIE.parasmooth
diff --git a/tests/gold/run_whiscy.sh b/tests/gold/run_whiscy.sh
index 95de003..57922f8 100755
--- a/tests/gold/run_whiscy.sh
+++ b/tests/gold/run_whiscy.sh
@@ -1,4 +1,4 @@
#!/bin/bash
-./whiscy 2SNIE.sur 2SNIE.conv 2SNIE.phylseq 2SNIE.out 2>&1 | awk 'NR > 8' > 2SNIE.whiscy
+./whiscy 2SNIE.sur 2SNIE.conv 2SNIE.phylseq 2SNIE.out 2>&1 | awk 'NR > 8' >2SNIE.whiscy
#./whiscy 2SNIE.sur 2SNIE.conv 2SNIE.phylseq 2SNIE.out
diff --git a/tests/test_consadjust_regression.py b/tests/test_consadjust_regression.py
index 2a734a9..60478d0 100644
--- a/tests/test_consadjust_regression.py
+++ b/tests/test_consadjust_regression.py
@@ -1,8 +1,8 @@
import filecmp
+import os
import subprocess
-from pathlib import Path
import sys
-import os
+from pathlib import Path
import pytest
diff --git a/tests/test_parasmooth_regression.py b/tests/test_parasmooth_regression.py
index 5825d50..c35a2e9 100644
--- a/tests/test_parasmooth_regression.py
+++ b/tests/test_parasmooth_regression.py
@@ -1,8 +1,8 @@
import filecmp
-import sys
+import os
import subprocess
+import sys
from pathlib import Path
-import os
import pytest
diff --git a/tests/test_resdist_regression.py b/tests/test_resdist_regression.py
index dbeb148..137e851 100644
--- a/tests/test_resdist_regression.py
+++ b/tests/test_resdist_regression.py
@@ -1,13 +1,12 @@
+import os
import subprocess
import sys
-import os
from pathlib import Path
import pytest
from . import GOLDEN_DATA_PATH
-
env = os.environ.copy()
env["PYTHONPATH"] = str(
Path(Path(__file__).parent.parent, "src"),
diff --git a/tests/test_whiscy_regression.py b/tests/test_whiscy_regression.py
index 18cbcf5..8e6ba5a 100644
--- a/tests/test_whiscy_regression.py
+++ b/tests/test_whiscy_regression.py
@@ -1,8 +1,6 @@
import filecmp
import os
-import shutil
import subprocess
-import os
import sys
from pathlib import Path