perl-utils

Custom Perl based utilities

1. Apply Rich Text Formatting to a Spreadsheet (xlsx)

Create an excel spreadsheet with data from a tab-delimited text file and apply custom text formatting to specified columns.

Using the 'text color' and 'underline' properties, highlight a specific sub string.

1. Requirements

   Excel::Writer::XLSX

2. Usage

   perl table-to-spreadsheet.pl <input table delimited file> <output directory <output file prefix>

   Input

   

   Output

   

2. Calculate variant allele frequency from a multi-sample VCF file

1. Usage

   perl allele-frequency.pl --vcf VCF_FILE [--out OUTPUT_FILE] [--withnames]

   Output:

   By default, the output will contain the following coulms and will be displayed on stdout:

   • CHR
   • POS
   • REF
   • ALT
   • ALLELE_FREQ
   • TOTAL_GENOTYPE
   • TOTAL_HET
   • TOTAL_HOM
   • SAMPLE_NAME(s) (included if --withnames parameter is specified)

   If the --out parameter is specified, the output will be writen to a file.

   Use as an executable binary:

   curl -o freq https://raw.githubusercontent.com/maurya-anand/perl-utils/refs/heads/main/allele-frequency/allele-frequency.pl && chmod +x freq

   ./freq --vcf VCF_FILE [--out OUTPUT_FILE] [--withnames]