From 6cb1fdfcf3758d96316afc86abc5b801ff6a2282 Mon Sep 17 00:00:00 2001
From: Kathy <37816304+kathy-snider@users.noreply.github.com>
Date: Wed, 10 Mar 2021 08:27:16 -0800
Subject: [PATCH] Explain patterns.

---
 README.md | 29 ++++++++++++++---------------
 1 file changed, 14 insertions(+), 15 deletions(-)

diff --git a/README.md b/README.md
index c7d4315..f71fc34 100755
--- a/README.md
+++ b/README.md
@@ -6,27 +6,26 @@
 
 The JSON file contains 2 elements:
   * The directory tree of the folder being cleaned in the "file_system_data" of
-  * the json. This is the "rules" portion that tells the script what to do (keep
-  * or delete) for each file and folder. The tree must match the directory tree
-  * of the folder being cleaned.
+  the json. This is the "rules" portion that tells the script what to do (keep
+  or delete) for each file and folder. The tree must match the directory tree
+  of the folder being cleaned.
   * The "pattern_list" whose value is a list of pattern strings.
 
 ## Patterns
 > If the data to be cleaned contains numbered files or folders, you can choose
-> to apply a rule (keep or delete) for one numbered file to all matching,
-> numbered files and folders.
+to apply a rule (keep or delete) for one numbered file to all matching,
+numbered files and folders.
 
 To do this, either add a pattern to the "pattern_list" or use the pattern flag
 in the cleaning script, below.
 
 #### Example 1
 > You have BIDS data and a lot of files and folder contain strings like
-> "task-rest_run-01". You don't know how many runs there are going to be, but
-> you want the rules for all task-rest runs to be the same.
- * Put rules in your tree for files and folders whose names contain
- * "task-rest_run-01".
+"task-rest_run-01". You don't know how many runs there are going to be, but
+you want the rules for all task-rest runs to be the same.
+ * Put rules in your tree for files and folders whose names contain "task-rest_run-01".
  * Add the pattern "task-rest_run-\*" to the list value of the "pattern_list"
- * element. (The \* is shorthand for all numbers.)
+element. (The \* is shorthand for all numbers.)
 
 All rules containing "task-rest_run-" followed by any number will be applied to
 all files and folders whose names contain "task-rest_run-" followed by any
@@ -38,9 +37,9 @@ patterns until you get used to them.
 
 #### Example 2
 > There is a set of files in your data called temp01, temp02, .... Again, you
-> don't know how many there will be, but you want them all gone.
+don't know how many there will be, but you want them all gone.
 * Make a rule for a file called temp0 (or temp6 or temp382 - doesn't matter,
-* just temp followed by a number). Set the value of its "state" to "delete".
+just temp followed by a number). Set the value of its "state" to "delete".
 * Add a pattern to the list for "temp*".
 
 Don't worry, all of your files with "template" in their names will not
@@ -49,7 +48,7 @@ disappear. Only files with the string "temp" followed directly by a number.
 
 ## CustomClean Cleaning Script (`cleaning_script.py`)
 > Delete things in a given directory based on the rules and patterns given in
-> the JSON.
+the JSON.
 
 Required arguments:
   * -j --json [path to JSON]
@@ -66,8 +65,8 @@ of the target directory.
 
 ## CustomClean GUI
 > **NOTE** As of 2.0.0, the cleaning script does not work with JSON files
-> created by the CustomClean GUI. To use the GUI and a cleaning script, use an
-> older version of CustomClean (pre 2.0.0). We hope to remedy this soon!
+created by the CustomClean GUI. To use the GUI and a cleaning script, use an
+older version of CustomClean (pre 2.0.0). We hope to remedy this soon!
 
 ## Installation
 1. Requires Python.