update script to new versions

Author: shiltemann

README.md

@@ -10,7 +10,11 @@ TAPscan (perl) script to detect TAPs (Transcription Associated Proteins) in your
 
 ## Quickstart
 
-See the `test-data` folder for example data and TAPscan run script.
+The `test-data` folder contains example data (input and output). To run TAPscan on this folder, use the `tapscan_run.sh` script.
+
+```
+./tapscan_run.sh test-data
+```
 
 ## Usage
 

tapscan_run.sh

@@ -1,6 +1,11 @@
 #!/usr/bin/env bash
 # USAGE: tapscan_run.sh path/to/folder/with/fastafiles
 
+tapscan_script='./tapscan_classify_v4.76.pl'
+domains="domains_v13.txt"
+rules="rules_v82.txt"
+coverage="coverage_values_v11.txt"
+
 # use current directory if none supplied as parameter
 seqfolder=${1:-.}
 
@@ -14,18 +19,18 @@ NAME=$(basename $i .fa)
 
 # run HMMr search
 echo "Running HMMsearch for $NAME"
-hmmsearch --domtblout "$NAME.domtblout" --cut_ga domains_v12.txt "$i"
+hmmsearch --domtblout "$NAME.domtblout" --cut_ga $domains "$i"
 
 # run TAPscan script
 echo "Running TAPscan Classify for $NAME"
 
-./tapscan_classify.pl \
+$tapscan_script \
 "$NAME.domtblout" \
-rules_v81.txt \
+$rules \
 "$NAME.output.1.family_classifications.txt" \
 "$NAME.output.2.family_statistics.txt" \
 "$NAME.output.3.subfamily_classifications.txt" \
-coverage_values_v10.txt
+$coverage
 
 done
 shopt -u nullglob