fixed a crash of the SFA module in case the list of cInDels is empty

README.md

@@ -6,6 +6,7 @@ Variant calling is a process to identify differences between strains, accessions
 Sequence variants can be analyzed to predict their functional effects on encoded proteins based on available structural annotations.
 Many existing tools operate on a variant-by-variant basis, and per-variant functional impact predictions are generally considered accurate.
 However, challenging cases arise where multiple neighboring variants must be considered simultaneously, especially when these variants influence each other's functional impact.
+
 The Neighborhood-Aware Variant Impact Predictor (NAVIP) addresses this problem by considering all variants that may affect a coding sequence (CDS) during the prediction process.
 This comprehensive approach increases the accuracy of predicting functional consequences by considering the broader genomic context surrounding the target variants.
 To use NAVIP, users must provide a Variant Call Format (VCF) file, a genomic FASTA file, and an associated Gene Feature Format (GFF3) file as input.
@@ -14,11 +15,10 @@ The tool is also freely available on our web server at: https://pbb-tools.de/NAV
 # Usage
 
 For the main program, there are no strict dependencies other than Linux, [Python 3](https://www.python.org), and [matplotlib](https://matplotlib.org).
-For most use cases, it is sufficient to download the source code / clone the git repository and
-run the script ***runnavip.sh*** with the required arguments, which will guide the user through the entire NAVIP processing pipeline:
+For most use cases, it is sufficient to download the source code / clone the git repository and run the script ***runnavip.sh*** with the required arguments, which will guide the user through the entire NAVIP processing pipeline:
 
 ```
-Usage: runnavip.sh --i <invcf> --g <ingff> --f <infasta> --o <outpath>
+Usage: runnavip.sh -i <invcf> -g <ingff> -f <infasta> -o <outpath>
 
 where:
    -i | --invcf   Specify the input VCF file

Readme.txt

@@ -1,52 +1,47 @@
-NAVIP has three existing modules: \
-1) VCF preprocessing, 
-2) the NAVIP main program, \
-3) and one simple first analysis of the created data.
-
+NAVIP has three existing modules:
+ 1) VCF preprocessing,
+ 2) the NAVIP main program,
+ 3) and one simple first analysis of the created data.
 
 You can choose the module with "--mode <module>".
-The module shortcuts are "pre","main" and "sfa" and there is a vcf-format-check "vcfc".
+The module shortcuts are "pre", "main" and "sfa" and there is a vcf-format-check "vcfc".
 
-For the VCF-Check: "--mode vcfc --invcf <path_with_file>"
 
-VCF preprocessing needs two more arguments:
+The VCF-Check needs one argument:
+ "--invcf <path_with_file>"
 
- "--invcf <path_with_file>" and "--outpath <path_to_folder>" 
+VCF preprocessing needs two arguments:
+ "--invcf <path_with_file>" and "--outpath <path_to_folder>"
 
-Please be aware, that no new folder will be created. 
+Please be aware, that no new folder will be created.
 
 The NAVIP main program needs four arguments:
+ "--invcf <path_with_file>", "--ingff <path_with_file>", "--infasta <path_with_file>" and "--outpath <path_to_folder>"
 
-"--invcf <path_with_file>", "--ingff <path_with_file>", "--infasta <path_with_file>" and "--outpath <path_to_folder>"
-
-The best possible output will be available, when the VCF file is 'corrected' by the preprozessing. However, NAVIP will still be able to deal with most of the 'normal' VCF data and will do its best.
+The best possible output will be available, when the VCF file is 'corrected' by the preprozessing.
+However, NAVIP will still be able to deal with most of the 'normal' VCF data and will do its best.
 
 The SFA module needs three arguments:
+ "--innavipvcf <path_with_file>", "--innavipfasta <path_with_file>" and "--outpath <path_to_folder>"
 
-"--innavipvcf <path_with_file>","--innavipfasta <path_with_file>" and "--outpath <path_to_folder>"
 
 Example: VCF preprocessing:
-
-"python3 navip.py \
---mode pre \
---invcf /.../small_variants.vcf \
---outpath /.../VCF_Preprocessing/"
-
+python3 navip.py \
+ --mode pre \
+ --invcf /.../small_variants.vcf \
+ --outpath /.../VCF_Preprocessing/
 
 Example: NAVIP main:
-"python3 navip.py \
---mode main \
---invcf VCF_Preprocessing/first.vcf \
---ingff /.../Araport11_GFF3_genes_transposons.201606.gff \
---infasta /.../TAIR10.fa \
---outpath /.../NAVIP_Main_Output/"
-
+python3 navip.py \
+ --mode main \
+ --invcf VCF_Preprocessing/first.vcf \
+ --ingff /.../Araport11_GFF3_genes_transposons.201606.gff \
+ --infasta /.../TAIR10.fa \
+ --outpath /.../NAVIP_Main_Output/
 
 Example: SFA:
-"python3 navip.py \
---mode sfa \
---innavipvcf /.../All_VCF.vcf \
---innavipfasta /.../all_transcripts_data.fa \
---outpath /.../SFA_Output/"
-
-
+python3 navip.py \
+ --mode sfa \
+ --innavipvcf /.../All_VCF.vcf \
+ --innavipfasta /.../all_transcripts_data.fa \
+ --outpath /.../SFA_Output/

compensating_indels.py

@@ -484,7 +484,8 @@ def find_all_cindels_v2(navip_vcf_file_link: str, mod_or_not: bool, outputfolder
 		table_output_file.write(description + "\n".join(normal_output_with_zeros))
 		table_output_file.close()
 
-		do_magic_plotting(normal_output_with_zeros,outputfolder, table_outputname,formats, max_x_axis_bpr )
+		if normal_output_with_zeros:
+			do_magic_plotting(normal_output_with_zeros,outputfolder, table_outputname,formats, max_x_axis_bpr )
 
 		### write all tids and stuff
 		involved_tid_list_output = []
@@ -557,7 +558,9 @@ def find_all_cindels_v2(navip_vcf_file_link: str, mod_or_not: bool, outputfolder
 		table_output_file = open(outputfolder + table_outputname, 'w')
 		table_output_file.write(description + "\n".join(normal_output_with_zeros))
 		table_output_file.close()
-		do_magic_plotting(normal_output_with_zeros, outputfolder, table_outputname,formats, max_x_axis_bpr)
+
+		if normal_output_with_zeros:
+			do_magic_plotting(normal_output_with_zeros, outputfolder, table_outputname,formats, max_x_axis_bpr)
 
 		### write all tids and stuff
 		involved_tid_list_unique = []

runnavip.sh

@@ -1,7 +1,7 @@
 #!/bin/sh
 
 help="
-  Usage: $(basename "$0") --i <invcf> --g <ingff> --f <infasta> --o <outpath>
+  Usage: $(basename "$0") -i <invcf> -g <ingff> -f <infasta> -o <outpath>
   
   where:
      -i | --invcf   Specify the input VCF file

sfa2.py

@@ -10,5 +10,6 @@ def sfa2_main(navip_vcf_file_link:str, mod_or_not:bool, outputfolder:str ,format
 	#def find_all_cindels_v2(navip_vcf_file_link: str, mod_or_not: bool, outputfolder: str, formats:str):
 	print("Starting compensating_indels script")
 	time = datetime.now()
-	cindels.find_all_cindels_v2(navip_vcf_file_link, mod_or_not, outputfolder, formats, max_x_axis_bpr)
-	print("Finished in: " +str(datetime.now() - time))
+	try:   cindels.find_all_cindels_v2(navip_vcf_file_link, mod_or_not, outputfolder, formats, max_x_axis_bpr)
+	except: import sys; print("Warning: List of cInDels is empty, skipping the analysis...", file=sys.stderr)
+	print("Finished in: " +str(datetime.now() - time))