Fix gzipped file load

cumc · Oct 31, 2023 · a6dea32 · a6dea32
1 parent 8184f91
commit a6dea32
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/variant-annotation/vep.ipynb b/variant-annotation/vep.ipynb
@@ -7,7 +7,7 @@
  "kernel": "SoS"
  },
  "source": [
- "# VEP annotation of rare variants using plugins"
+ "# VEP annotation of variants in VCF format using plugins"
  ]
  },
  {
@@ -314,7 +314,7 @@
  " header = header_comment.split('#')[1]\n",
  " # Split the header into column names\n",
  " columns = header.split('\\t')\n",
- " df = pd.read_csv(${_input}, comment='#', sep='\\t', names=columns)\n",
+ " df = pd.read_csv(${_input}, compression='gzip', comment='#', sep='\\t', names=columns)\n",
  " df.to_csv(${_output}, index=False, sep='\\t', header=True, compression={'method': 'gzip', 'compresslevel': 9})"
  ]
  },