Dear All
I have two input files. I want to search an element of File1 in File 2. If the
condition matched, print out something.
File1:
scaffold_1_541600 0.856102487445412 0.295040551475357
0.795878312070658 312
The element used to search is 541600,
File2:
scaffold_1 phytozome8_0 gene 540839 544291 . -
ID=POPTR_0001s00630;Name=POPTR_0001s00630
If 541600 is between the four and five elements of File2 (between 540839 and
544291), print out the line in File 1 and followed by genename (the last
element of file 2).
My script is as follows. And usage is: ./myscript.pl FstFile.txt
annotationFile.txt
# USAGE:
# unix command line:
# ./searchAndPrint.pl FstFile.name annotationFile.name
#!/usr/bin/perl -w
use strict;
use warnings;
my $FstFile = shift @ARGV; # read file names from terminal input
my $annotationFile = shift @ARGV;
open FST, '<', $FstFile or die "Cannot open '$FstFile' because: $!";
open ANNO, '<', $annotationFile or die "Cannot open '$annotationFile' because:
$!";
my $outfile = "criticalFstChr1WithGeneName.txt";
open OUT, '>', $outfile or die "Cannot open '$outfile' because: $!";
print OUT "pos\tFit\tFst\tFis\tgene\n";
my @genename;
my @startSite;
my @stopSite;
while(<ANNO>) {
chomp;
next if /^#/;
my @tmpo=split("\t",$_);
#@tmpo = grep $tmpo[0] eq 'scaffold_1', @tmpo;
#@tmpo = grep $tmpo[2] eq 'gene', @tmpo;
if (($tmpo[0] eq 'scaffold_1') && ($tmpo[2] eq 'gene')){
push(@genename, $tmpo[8]);
push(@startSite, $tmpo[3]);
push(@stopSite, $tmpo[4]);
}
}
while(<FST>) {
next if /^Fit/;
chomp;
my @tmp=split("\t",$_);
$tmp[0]=~s/\_/>/g;
my @dat=split(">",$tmp[0]);
for(my $i=0; $i <= length(@startSite)-1; $i++) {
if (($dat[2] >= $startSite[$i]) && ($dat[2] <= $stopSite[$i])){
print OUT "$tmp[0]\t$tmp[1]\t$tmp[2]\t$tmp[3]\t$genename[$i]\n";
last;
}
elsif (($dat[2] > $stopSite[$i]) && ($dat[2]< $startSite[$i+1])){
print OUT "$tmp[0]\t$tmp[1]\t$tmp[2]\t$tmp[3]\t'intergenicRegion'\n";
last;
}
}
}
close FST;
close ANNO;
close OUT;
But I got errors as follows:
./searchAndPrint.pl: line 6: use: command not found
./searchAndPrint.pl: line 7: use: command not found
./searchAndPrint.pl: line 9: my: command not found
./searchAndPrint.pl: line 10: my: command not found
The files /FST,, Cannot open '' because: do not exist.
The files /ANNO Cannot open '' because: do not exist.
./searchAndPrint.pl: line 16: my: command not found
The files /OUT Cannot open '' because: do not exist.
./searchAndPrint.pl: line 18: print: command not found
./searchAndPrint.pl: line 20: my: command not found
./searchAndPrint.pl: line 21: my: command not found
./searchAndPrint.pl: line 22: my: command not found
./searchAndPrint.pl: line 24: syntax error near unexpected token `)'
./searchAndPrint.pl: line 24: `while(<ANNO>) {'
It seems it doesnot recognize Perl. I feel very confused.
I got some help for the previously posted questions on the list and it helps me
improve a lot! Thank you guys!
All the best
Li
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