A python program to find the smallest fragments (i.e. the most likely to be amplified) from a set of primers in a target DNA sequence. The command generates a csv file (default: output.csv, use -o
or --output
to change) with 2 columns; 5' position of primer hit and length of fragment generated by the closest 3' primer site. The 5' position is the last base of the 5' primer. The length of fragment excludes the lengths of the two primers.
usage: primerFinder.py [-h] [-v] -i INPUTFILE -p PATTERNFILE [-o OUTFILE]
A program to find the smallest fragments (i.e. the most likely to be
amplified) from a set of primers in a target DNA sequence. The command
generates a csv file (default: output.csv, use `-o` or `--output` to change)
with 2 columns; 5' position of primer hit and length of fragment generated by
the closest 3' primer site. The 5' position is the _last_ base of the 5'
primer. The length of fragment excludes the lengths of the two primers.
optional arguments:
-h, --help show this help message and exit
-v, --verbose increase output verbosity
-i INPUTFILE, --inputFile INPUTFILE
file to find primers in (assumes the file contains
only DNA sequence, i.e. no headers, and that newlines
are not significant)
-p PATTERNFILE, --patternFile PATTERNFILE
primer file with one primer per line all 5' to 3'
-o OUTFILE, --outFile OUTFILE
file to write to
Example usage:
./primerFinder.py -i inputExample.txt -p primersExample.txt -v