Perl string concatenation overlaying strings

Question

I am trying to concatenate 3 strings in perl, and I am getting weird behavior. The data was just written to a file previously in the script, and I am trying to add two columns to the data.

Here is my code and its behavior

print "phylipId is $phylipId\n";
print "Tree is $tree\n";
print "Line is $line\n";

my $string = join "\t", $phylipId, $tree, $line;

print "Concatenated is $string\n";

Gives me this output

phylipId is 4
Tree is (138,((139,141),140));
Line is 000931  17.0    1.0 0.135   no  1044    646918204
Concaten000931s 17.0    1.08,((10.1351),no0));  1044    646918204

This also happened when I used the . operator. Any help would be appreciated

phemmer · Accepted Answer · 2012-03-24 06:33:18Z

4

It looks like youre reading $tree from a file using carriage-returns (\r), and $tree is ending up with \r at the end of it causing it to seek to the beginning of the line.

See this test:

perl -e 'print("abcdefghijkl\r\t012\n");'

Which outputs

abcdefgh012l

answered Mar 24, 2012 at 6:33

phemmer

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1 Comment

avs3323 Over a year ago

Yeah, this was the problem. I was generating the tree files using a template file that had been created in windows. I fixed the line endings for them and it works now, thanks

Borodin · Accepted Answer · 2012-03-24 18:41:58Z

1

As patrick says, it is more than likely you have read a DOS-formatted file on a Linux box. In those circumstances, if you use chomp on a string terminated with "\r\n" you will be left with the "\r".

The simplest way to clean up records like this is to replace chomp with

s/\s+$//

which, since both "\r" and "\n" count as whitespace, will remove both from the string simultaneously. If trailing tabs and spaces are important for you then use

s/[\r\n]+$//

instead, or perhaps

s/[[:cntrl:]]+$//

or

s/\p{Control}+$//

answered Mar 24, 2012 at 18:41

Borodin

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2 Comments

phemmer Over a year ago

If the file is known to have "\r\n" line endings, the clean way to so this is to set $/ = "\r\n" and then use chomp.

Borodin Over a year ago

@Patrick: My intention was to offer something that would work on all files regardless of origin, but you are absolutely right and that is what I would write.

Renaud Bompuis · Accepted Answer · 2012-03-24 06:16:52Z

0

I'm not able to replicate your issue after trying under Windows and Linux.

Could the issue be related to how your console is configured?
does it happen on other machines too?
Can you tell more about your exact environment?
What happens if you try to print that line to a text file instead of stdout?

answered Mar 24, 2012 at 6:16

Renaud Bompuis

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