I want to know how many times the string in 2nd column appears in the first column as substring.
Neither of the perl suggestions nor the ksh/egrep script handle this properly. They are all taking the second column and treating it as a regular expression. Should the text in that column contain any regexp metacharacters, they yield erroneous results. And if the text in the second column forms an invalid regular expression, they will error out.
Place a lone asterisk in the second column and you may see something similar to:
Code:
Quantifier follows nothing in regex; marked by <-- HERE in m/* <-- HERE / at substring.pl line 26, <> line 6.
Worse, a valid regular expression with metacharacters (.*) will silently return incorrect results. Perhaps your real data consists of nothing but alphanumerics, in which case the code provided should be adequate, but that wasn't made clear and your problem statement asks for fixed string matching.
Quote:
Originally Posted by polsum
Hi
I have a table like this
Code:
aaacgt cgt
cggaat acg
acgt
cgtgha
jhaja
I want to know how many times the string in 2nd column appears in the first column as substring.
For example the first string of 2nd column "cgt" occurs 3 times in the 1st column and "acg" one time.
So my desired output is
Code:
cgt 3
acg 1
THank you very much in advance
Quote:
Originally Posted by polsum
Thanks a lot for your replies. My file is not that big...it has 30000 rows. and It always has 2 columns.
The only sample data you've provided contradicts that statement; some of the lines have only one line.
Also, should the string appearing in the second column be searched for in column 1 of all rows or only rows that follow it? If only those that follow, does that include the current row? You should clarify, because you state above that "acg" only occurs once in column 1, and your desired output shows a 1 for "acg", but "acg" actually occurs twice in the first column.
All suggestions so far scan the entire column an in fact will return 2 where you say it should be 1.
Also, should the string occurring more than once in column1 of a single row be counted as one instance or multiple instances? One of the perl solutions and the ksh/egrep will count "acgacg" as one instance of "acg", while the remaining perl solution would count it as two instances.
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Thanks and Regards
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08-19-2011
