https://github.com/JuliaFlynn/PacBio_barcode_assocation
Tip revision: 29eac92475a9ff8e24fb390986c865b504c03f51 authored by JuliaFlynn on 26 May 2022, 22:22:57 UTC
Update README.md
Update README.md
Tip revision: 29eac92
pacbio5b.pl
#!/usr/bin/perl
#
if ($#ARGV!=1) {
print "usage: script.pl infile outfile\n";
exit;
}
$infile = $ARGV[0];
$outfile = $ARGV[1];
open(INF, $infile) ;
open(OUTF, ">$outfile") ;
open(REJECTF, ">reject5.out") ;
open(SUMF, ">sum5.out") ;
$nok=0;
$nbad=0;
$oldline="" ;
$oldbc="" ;
$midline="Y" ;
$midbc="X" ;
while ($newline = <INF>) {
chomp($newline) ;
@spline = split (/,/, $newline) ;
$newbc=$spline[0] ;
if ($midbc ne $oldbc and $midbc ne $newbc) {
print OUTF "$midline\n" ;
$nok++ ;
} else {
print REJECTF "$midline\n" ;
$nbad++ ;
}
$oldbc=$midbc;
$oldline=$midline;
$midbc=$newbc;
$midline=$newline;
}
print SUMF "ok $nok\n" ;
print SUMF "bad $nbad\n" ;
close(INF) ;
close(OUTF) ;
close(REJECTF) ;
close(SUMF) ;