Misc

list_files.py

This script will print(std out) all the fieldnames and field in the file path.

Input:

  • -p : file path to check

Output:

  • All the filenames and fields under CSV files in a specified path

Usage

  • python fastq-parser.py –version

This is the option that show you the program’s version.

  • python fastq-parser.py -h

This can show you some help information.

  • python fastq-parser.py -i <filename.fastq>

Runs program with specified file path

list_files.get_fieldnames(pattern_to_check)

Get all fieldnames of CSV files in a given path

list_files.main()

Find and print fieldnames

list_files.print_fieldnames(fieldnames_to_print)

Print all fieldnames given a list of fieldnames to print

sas7bdat_to_csv.py

This script will transfer a .sas file to a .csv file.

Input:

  • -i : input sas7bdat file

  • -o : desired output CSV file

  • -d : deliminator to write between columns in output file OPTIONAL

Output:

  • sas7bdat file as CSV file, with possible deliminator between columns

Usage:

  • python sas7bdat_to_csv.py –version

  • This is the option that show you the program’s version.*

  • python sas7bdat_to_csv.py -h

  • This can show you some help information.*

  • python sas7bdat_to_csv.py -i <input.sas7bdat> -o <output.csv> -d <deliminator>

  • Runs the program with specified input file, output file, and deliminator.*

sas7bdat_to_csv.main()

Transfer a .sas7bdat file to a .csv file.

xml_parser.py

This script will print(std out) some domains of a .xml file.

Input:

  • -i : specified input file

Output:

  • Some domains of a .xml file

Usage:

  • python xml-parser.py –version

  • This is the option that show you the program’s version.*

  • python xml-parser.py -h

  • This can show you some help information.*

  • python xml-parser.1.py -i <filename.xml>

Runs program with specified input file

xml_parser.main()

Finds and prints XML domains

vcf_reformatter.py

Script will reprocess the vcf output of a HIVE Heptagon file to be in the appropriate vcf file format per the standard.

Input:

  • -i : specified file to reformat

  • -o : specified output file

Output:

  • Reformed vcf file

Usage:

  • python vcf_reformatter.py –version

This is the option that show you the program’s version.

  • python vcf_reformatter.py -h

This can show you some help information.

  • python vcf_reformatter.py -i <input.vcf> -o <output.vcf>

Runs the program with specified input file, output file

vcf_reformatter.chrom_grabber(inline)

Function to grab the chromosome number from the line, given HIVE’s output style

vcf_reformatter.main()

Read through file, ignore the headers, grab all of the relevant information, print it out in VCF format.