Extract strings between two separators using regex in perl - regex

Question

I have a file which looks like:
uniprotkb:Q9VNB0|intact:EBI-102551 uniprotkb:A1ZBG6|intact:EBI-195768
uniprotkb:P91682|intact:EBI-142245 uniprotkb:Q24117|intact:EBI-156442
uniprotkb:P92177-3|intact:EBI-204491 uniprotkb:Q9VDK2|intact:EBI-87444
and I wish to extract strings between : and | separators, the output should be:
Q9VNB0 A1ZBG6
P91682 Q24117
P92177-3 Q9VDK2
tab delimited between the two columns.
I wrote in unix a perl command:
perl -l -ne '/:([^|]*)?[^:]*:([^|]*)/ and print($1,"\t",$2)' <file>
the output that I got is:
Q9VNB0 EBI-102551 uniprotkb:A1ZBG6
P91682 EBI-142245 uniprotkb:Q24117
P92177-3 EBI-204491 uniprotkb:Q9VDK2
I wish to know what am I doing wrong and how can I fix the problem.
I don't wish to use split function.
Thanks,
Tom.

Answer 1

The expression you give is too greedy and thus consumes more characters than you wanted. The following expression works on your sample data set:
perl -l -ne '/:([^|]*)\|.*:([^|]*)\|/ and print($1,"\t",$2)'
It anchors the search with explicit matches for something between a ":" and "|" pair. If your data doesn't match exactly, it should ignore the input line, but I have not tested this. I.e., this regex assumes exactly two entries between ":" and "|" will exist per line.

Answer 2

Try m/: ( [^:|]+ ) \| .+ : ( [^:|]+ ) \| /x instead.

Answer 3

A fix could be to use a greeding expression between the first string and the second one. With .* it goes until the end and begins to backtrack searching for the last colon followed by a pipe.
perl -l -ne '/:([^|]*).*:([^|]*)\|/ and print($1,"\t",$2)' <file>
Output:
Q9VNB0 A1ZBG6
P91682 Q24117
P92177-3 Q9VDK2

Answer 4

See it in action:
:([\w\-]*?)\|
Another method:
:(\S*?)\|

Answer 5

The way you've specified it, it has to match that way. You want a single colon
followed by any number of non-pipe, followed by any number of non-colon.
single colon -> :
non-pipe -> Q9VNB0
non-colon -> |intact
colon -> :
non-pipe -> EBI-102551 uniprotkb:A1ZBG6
Instead I make a space the end-of-contract, and require all my patterns to begin
with a colon, end with a pipe and consist of non-space/non-pipe characters.
perl -M5.010 -lne 'say join( "\t", m/[:]([^\s|]+)[|]/g )';

Answer 6

perl -nle'print "$1\t$2" if /:([^|]*)\S*\s[^:]*:([^|]*)/'
Or with 5.10+:
perl -nE'say "$1\t$2" if /:([^|]*)\S*\s[^:]*:([^|]*)/'
Explanation:
: Matches the start of the first "word".
([^|]*) Matches the desired part of the first "word".
\S* Matches the end of the first "word".
\s+ Matches the "word" separator.
[^:]*: Matches the start of the second "word".
([^|]*) Matches the desired part of the second "word".
This isn't the shortest answer (although it's close) because each part is quite independent of the others. This makes it more robust, less error-prone, and easier to maintain.

Answer 7

Why do you not want to use the split function. On the face of it this would be easily solved by writing
my #fields = map /:([^|]+)/, split
I am not sure how your regex is supposed to work. Using the /x modifier to allow non-significant whitespace it looks like this
/ : ([^|]*)? [^:]* : ([^|]*) /x
which finds a colon and optionally captures as many non-pipe characters as possible. Then skips over as many non-colon characters as possible to the next colon. Then captures zero asm many non-pipe characters as possible. Because all of your matches are greedy, any one of them is allowed to consume all of the rest of the string as long as the characters match the character class. Note that a ? that indicates an optional sequence will first of all match all that it can, and the option to skip the sequence will be taken only if the rest of the pattern cannot then be made to match
It is hard to judge from your examples the precise criteria for a field, but this code should do the trick. It finds sequences of characters that are neither a colon nor a pipe that are preceded by a colon and terminated by a pipe
use strict;
use warnings;
while (<DATA>) {
my #fields = /:([^:|]+)\|/g;
print join("\t", #fields), "\n";
}
__DATA__
uniprotkb:Q9VNB0|intact:EBI-102551 uniprotkb:A1ZBG6|intact:EBI-195768
uniprotkb:P91682|intact:EBI-142245 uniprotkb:Q24117|intact:EBI-156442
uniprotkb:P92177-3|intact:EBI-204491 uniprotkb:Q9VDK2|intact:EBI-87444
output
Q9VNB0 A1ZBG6
P91682 Q24117
P92177-3 Q9VDK2