Script to run an in silico pcr for a set of primer pairs on an assembly
REQUIREMENTS:
Requires tre approximate regex module https://github.com/laurikari/tre/ to be in your path
USAGE:
in_silico_pcr.py [options] fasta/multifasta input files
Options:
-h, --help show this help message and exit
-p FILE, --primers=FILE
text file containing primers. For each region of
interest there should be one row. Each row should
contain 3 or 5 whitespace-delimited columns: 1) Name
of the region, 2) forward primer sequence, 3) reverse
primer sequence 4) maximum product length (optional)
5) minimum product length (optional, and can only be
included with 4). The file may contain a header row,
but if this is the case the -H option must be
specified (or strange things might happen)
-H, --header primer file has a header row [default=False]
-r, --rcreverse Reverse primers require reverse complementing (use
this option if your reerse primers are in the same
direction as your forward primers) [default=False]
-i, --incprimer include primer sequence in fasta output
[default=False]
-m MAXCOST, --maxcost=MAXCOST
maximum cost (number of changes in a primer sequences)
allowed for a valid match. [Default= 3]
-o PREFIX, --prefix=PREFIX
output file prefix
-e, --potentials include potential primer locations in tab files in
cases where no pair within selected product size range
is found [default=False]
-c, --circular sequences are circular [default=False]