Use subprocessPopen to make a script that connects the first

Use subprocess.Popen to make a script that connects the first 3 fastx/fastq data cleaning commands

Instead of sending output from fastq_quality_filter on to the trimmer, make it an iterable, send it to your own fastq parser, and filter for length!!!

The script should gather input parameters from a command line using any of the methods we learned last week.

Solution

-min_len <integer>

        Filter sequence shorter than min_len.

-max_len <integer>

        Filter sequence longer than max_len.

my @aux = undef;

while (my ($name, $seq, $qual) = readfq(\\*STDIN, \\@aux)) {

     if( (length($seq) >= 21) && (length($seq) <= 25) ) {

         print \"@$name\ \";

         print \"$seq\ \";

         print \"+\ \";

         print \"$qual\ \";

     }

}