From 48eed12db2367dfdfbdf79bd16533f7335a8c647 Mon Sep 17 00:00:00 2001
From: Jethro Rainford <rainford1995@gmail.com>
Date: Fri, 20 Sep 2024 10:11:25 +0100
Subject: [PATCH] improve prints

---
 src/vcf_qc.py | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/src/vcf_qc.py b/src/vcf_qc.py
index 4c168cd..ad54ed8 100644
--- a/src/vcf_qc.py
+++ b/src/vcf_qc.py
@@ -111,6 +111,8 @@ def get_het_hom_counts(vcf) -> dict:
         'x_hom': []
     }
 
+    variants = autosomes = x_variants = 0
+
     for record in vcf_handle.fetch():
         sample_fields = record.samples[sample]
 
@@ -122,6 +124,8 @@ def get_het_hom_counts(vcf) -> dict:
         if sample_fields['GT'] == (0, 0):
             continue
 
+        variants += 1
+
         # using the sum of all allele depths instead of the format AD
         # field to be the informative read depths supporting each allele
         informative_total_depth = sum(sample_fields['AD'])
@@ -132,16 +136,20 @@ def get_het_hom_counts(vcf) -> dict:
         if len(set(sample_fields['GT'])) == 1:
             # homozygous variant
             if is_autosome(record.chrom):
+                autosomes += 1
                 counts['hom'].append(non_ref_aaf)
 
             if re.match(r'(chr)?x', record.chrom, re.IGNORECASE):
+                x_variants += 1
                 counts['x_hom'].append(non_ref_aaf)
         else:
             # heterozygous variant
             if is_autosome(record.chrom):
+                autosomes += 1
                 counts['het'].append(non_ref_aaf)
 
             if re.match(r'(chr)?x', record.chrom, re.IGNORECASE):
+                x_variants += 1
                 counts['x_het'].append(non_ref_aaf)
 
         # handy print for the logs for sense checking
@@ -152,6 +160,11 @@ def get_het_hom_counts(vcf) -> dict:
             f"\tAAF: {non_ref_aaf}"
         )
 
+    print(
+        f"\nTotal variants: {variants}\nTotal autosome variants: {autosomes}\n"
+        f"Total X variants: {x_variants}\n"
+    )
+
     return {k: sorted(v) for k, v in counts.items()}
 
 
@@ -199,7 +212,7 @@ def calculate_ratios(counts) -> dict:
     )
 
     for field, value in ratios.items():
-        print(f"{field}\t{value}")
+        print(f"{field}:\t{value}")
 
     return ratios
 
@@ -254,7 +267,7 @@ def upload_output_file(outfile) -> None:
     outfile : str
         name of file to upload
     """
-    print(f"Uploading {outfile}")
+    print(f"\nUploading {outfile}")
 
     url_file = dxpy.upload_local_file(
         filename=outfile,