add README.md

TheSergeyPixel · Nov 18, 2022 · b0dd0bd · b0dd0bd
1 parent 3de0b7c
commit b0dd0bd
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/README.md b/README.md
@@ -30,8 +30,10 @@ We are currently working on creating conda package.
 
 ## Usage
 
-Diablo G25 requires basic **gzipped** VCF file (for example, HaplotypeCaller + GenotypeGVCFs output) as input. The 
-output is always generated as tsv file. Run main.py from downloaded repository as follows:
+Diablo G25 requires basic **gzipped** VCF file (for example, HaplotypeCaller + GenotypeGVCFs output) as input.
+Important to note, that **VCF has to be annotated with rsID** in ID column (e.g with GATK VariantAnnotator). <br/>
+ <br/>
+The output is always generated as tsv file. Run main.py from downloaded repository as follows:
 
 ```
 python main.py -i /path/to/vcf/file.vcf -o /desired/output/direcotry/output.tsv -m model_name

diff --git a/main.py b/main.py
@@ -101,7 +101,8 @@ def main():
     mod_scores = admix(os.path.abspath(args.output), args.model)
 
     with open(os.path.join(os.path.split(args.output)[0],
-                           f"{''.join(os.path.split(args.output)[1].split('.')[:-1])}_G25.tsv"), 'w') as g_scores:
+                           f"{''.join(os.path.split(args.output)[1].split('.')[:-1])}_{args.model}.tsv"), 'w') \
+            as g_scores:
         g_scores.write(f"{''.join(os.path.split(args.output)[1].split('.')[:-1])},{mod_scores}")
 
     stop_time = time()