Perl Command : Add A Column With Strand Information

Question

[biolab]

Dear all,

i have a blast output file and need to add a column for strand infromation (+ or -). For example,

gene1 contig2 1 69 100 169
gene2 contig20 3 53 250 200

i need to change it to

gene1 contig2 1 69 100 169 +
gene2 contig20 3 53 250 200 -

note: 100<169 +, 250>200 -

i am new in perl programming. my command is $ cat a.txt | perl -e 'while (<>){chomp; @array = split(//, $_); if ($array[4]< $array[5]){print"@array\t+\n"} else {print"@array\t-\n"} }'

The output is

g e n e -   c o n t i g 2   1   6 9   1 0 0   1 6 9
g e n e -   c o n t i g 2 0   3   5 3   2 5 0   2 0 0

Could anyone help to correct the errors and briefly describe it? Thank you very much!!

[Michael]

try: replace @array = split(//, $_); with @array = split(/\s/, $_); or simply @array = split;

[biolab]

thank you very much for correction.

Answer 1

[SES]

Here's a simpler Perl solution (similar to the Awk solution of Frédéric Mahé):

$ echo -e 'gene1 contig2 1 69 100 169\ngene2 contig20 3 53 250 200' \
| perl -ane 'print join "\t", @F, $F[4] > $F[5] ? "-\n" : "+\n"'
gene1    contig2     1    69    100    169    +
gene2    contig20    3    53    250    200    -

You could make it perhaps more readable by adding explicit loops and variables, but for one-liners I think it's best to use the tools you have and save yourself some typing.

EDIT: Perl's command line switches are documented in perlrun (typeperldoc perlrun from the command line).

• The -e tells Perl to process the command line arguments, which would be any files or STDIN (as is the case above).
• The -n switch will make Perl loop over the input line by line (the -p does the same, but turns on an implicit print).
• The -a tells Perl to autosplit the input and put it into an array called "@F" when used with -n or -p. You can change the delimiter with the -F switch.

[biolab]

Thank you! The shorter perl command is really cool.

[biolab]

Hi, SES, can i ask you one more question? What's the -ane option stands for? Would you please breifly introduce these functions to me, as I googled perl -ane, but did not find an answer. Thank you very much!

[SES]

I updated my post and to add an explanation of the command.

[biolab]

Your explanations are really informative and help me learn perl. Thanks!

Answer 2

[PoGibas]

Simple awk solution awk '{if ($5>$6) print $0,"-"; else print $0,"+"}' INPUT

echo -e 'gene1 contig2 1 69 100 169\ngene2 contig20 3 53 250 200' |  awk '{if ($5>$6) print $0,"-"; else print $0,"+"}'
>gene1 contig2 1 69 100 169 +  
gene2 contig20 3 53 250 200 -

[Frédéric Mahé]

Hi Pgibas, in Awk if-then-else conditional can be eventually replaced with a ternary operator (shorter but maybe less clear):

echo -e 'gene1 contig2 1 69 100 169\ngene2 contig20 3 53 250 200' | awk '{print $0,($5 > $6) ? "-" : "+"}'

[PoGibas]

Thank you, this is really cool

[biolab]

Thank you very much for your solutions!