Scripts

CSV Scripts

Scripts involving the manipulation of CSV Files

Includes the following functionalities:

  • Parse contents of a csv file to a list

  • Print fieldnames and the number of elements in each fieldname in a csv.

  • Add a new last column that is the product of the the third and fourth row.

  • Add double quotes to all values in a csv file

FASTA/FASTQ Scripts

Scripts involving the manipulation of fasta/fastq files

Includes the following functionalities:

  • Check if there are duplicate IDs in a fasta file

  • Print the sequence of a record with a given ID in a fasta file

  • Print the read_id, read_seq and read_qual from the input fastq file.

  • Parse the RVDB formatted FASTA headers so they can be interperated by HIVE-hexagon’s tablequery

Misc

Misc scripts

Includes the following functionalities:

  • Print all the fieldnames and field in the file path.

  • Transfer a .sas7bdat file to a .csv file

  • Convert a VCF file generated by HIVE Heptagon into the VCF standard to be compatible with other applications.