I have a long file of text strings, sorted by length. What I need to do is find any short lines contained within long lines, breaking up the long line into two shorter lines, and leaving the original short line intact, like this:
input:
here is an example of a long line
an example of
output:
here is
a long line
an example of
You haven't posted sufficient dataset to allow us to post a complete solution, but here is something to get you started:
$ awk '
NR==FNR{
a[$0]++;
next
}
{
for(x in a)
if(x!=$0 && index($0,x)>0) {
sub(x FS,"\n")
}
}1' file file
here is
a long line
an example of
We are doing two passes to the file. In the first pass, read the lines and store them as key in an array (duplicate lines will get stored as one key).
In the second pass, we iterate through the array, if the key is not equal to the current line but is a subset of the current line, substitute that smaller word with a newline.
Related
probably a simple issue, but I cannot seem to solve it like this.
I want to replace the headers of a FASTA file. This file is a subset of a larger file, but headers were adjusted in the process. I want to add the original headers since it includes essential information.
I selected the headers from the subset (subset.fasta) using grep, and used this to match and extract the headers from the original file, giving 'correct.headers'. They are the same number of headers and in the same order, so this should be ok.
I found the code below which should do what I want according to the description. I've only started learning awk, so I can't really control it, though.
awk 'NR == FNR { o[n++] = $0; next } /^>/ && i < n { $0 = ">" o[i++] } 1' correct.headers subset.fasta > subset.correct.fasta
(source: Replace fasta headers using sed command)
However, there are some 100 more output lines than expected, and there's a shift starting after a couple of million lines.
My workflow was like this:
I had a subsetted fasta-file (created by a program extracting certain taxa) where the headers were missing info:
>header_1
read_1
>header_2
read_2
...
>header_n
read_n
I extracted the headers from this subsetted file using grep, giving the subset headers file:
>header_1
>header_2
...
>header_n
I matched the first part of the header to extract the original headers from the non-subsetted file using grep:
>header_1 info1
>header_2 info2
...
>header_n info_n
giving the same number of headers, matching order, etc.
I then used this file to replace the headers in the subset with the original ones using above awk line, but this gives a mismatch at a certain point and adds additional lines.
result
>header_1 info1
read_1
>header_2 info2
read_2
...
>header_x info_x
read_n
Where/why does it go wrong?
Thanks!
I am writing a pretty long AWK program (NOT terminal script) to parse through a network trace file. I have a situation where the next line in the trace file is ALWAYS a certain type of 'receive' (3 possible types) - however, I only want AWK to handle/print on one type. In short, I want to tell AWK if the next line contains a certain receive type, do not include it. It is my understanding that getline is the best way to go about this.
I have tried a couple different variations of getline and getline VAR via the manual, I still cannot seem to search through and reference fields in the next line like I want. Updated from edit:
if ((event=="r") && (hopSource == hopDest)) {
getline x
if ((x $31 =="arp") || (x $35 =="AODV")) {
#printf("Badline %s %s \n", $31, $35)
}
else {
macLinkRec++;
#printf("MAC Link Recieved from HEAD - %d to MEMBER %d \n", messageSource, messageDest)
}
}
I am using the print(badline) as just a marker to see what is going on. I fully understand how to restructure the code once I get the search and reference correct. I am also able to print the correct 'next' lines. However, I would expect to be able to search through the next line and create new arguments based on what is contained in the next line. How do I search a 'next line' based on an argument in AWK? How do I reference fields in that line to create new arguments?
Final note, the 'next line' number of fields (NF) varies, but I feel that the $35 field reference should handle any problems there.
There is a large file where the last symbols are \r\n. I need to remove them. It seems to be equivalent to removing the last line(?).
UPD: no, it's not: a file have only one line, which ends with \r\n.
I know two ways, but both don't work for AIX:
sed 's/\r\n$//' file # I don't why it doesn't work
head -c-2 # head doesn't work with negative numbers
Is there any solution for AIX? A lot of large files must be processed, so performance is important.
Usually, if you need to edit a file via a script in place, I use ed due to historical reasons. For example:
ed - /tmp/foo.txt <<EOF
g/^$/d
w
q
EOF
ed is more than a bit cantankerous. Note also that you did not really remove the empty lines at the bottom of the file but rather all of the empty lines. With ed and some practice you can probably achieve deleting only the empty lines at the bottom of the file. e.g. go to the bottom of the file, search up for a non-empty line, then move down a line and delete from that point to the end of the file. ed command scripts act (pretty much) as you would expect.
Also, if they really do have \r\n, then those are not going to be considered empty lines but rather lines with a control-M (\r) in them. You may need to adjust your pattern if that is the case.
My answer https://stackoverflow.com/a/46083912/3220113 to the duplicate question should work here too. Another solution is using
awk ' (NR>1) { print s }
{s=$0}
END { printf("%s",substr($2, 1, length($2)-1) ) }
' inputfile
I have a big Fasta file which I want to modify. It basically consists of many sequences with headers that start ">". My Problem is, that some of the Headers are not unique, even though the Sequences are unique.
Example:
>acrdi|AD19082
STSTAFPLLTQFYGCAIIILVLAMCCSCLVYAMYFMNSSGLQTHESTVTQKVKDFSLQ
WLQPILFGCSWRHRLIAKSRRNRSKIQPMTGTEPPWNESKDAFENLKTWALNKQNRNCLL
EINFLEAKDFIVMCKDVVCFEEDDKDERNLNLCLKTLTEAFRFLRNCCAETPKNQSFVIS
SGVAKQAIEVILILLRPVFQEREKGTEVITDTIRSGLQLLGNTVVKNIDTQEFIWNCCCP
QFFLDVLLSRHHSIQDCLCMIIFNCLNQQRRLQLVNNPKIISQIVHLCADKSLLEWGYFI
LDCLICEGLFPDLYQGMEFDPLARIILLDLFQVKITDALDESSERTERTETPKELYASSL
NYLAEQFETYFIDIIQRLQQLDYSSNDFFQVLVVTRLLSLLSTSTGLKSSMTGLQDRASL
LETCVDLLRETSKPEAKAAFKRPGTSYWEYVLPTFP
>acrdi|AD19082
MLRQSEPPWNESKDAFENLKTWALNKQNRNCLLEINFLEAKDFIVMCKDVVCFEEDDKDE
RNLNLCLKTLTEAFRFLRNCCAETPKNQSFVISSGVAKQAIEVILILLRPVFQEREKGTE
VITDTIRSGLQLLGNTVVKNIDTQEFIWNCCCPQFFLDVLLSRHHSIQDCLCMIIFNCLN
QQRRLQLVNNPKIISQIVHLCADKSLLEWGYFILDCLICEGLFPDLYQGMEFDPLARIIL
LDLFQVKITDALDESSERTERTETPKELYASSLNYLAEQFETYFIDIIQRLQQLDYSSND
FFQVLVVTRLLSLLSTSTGLKSSMTGLQDRASLLETCVDLLRETSKPEAKAAFSNVSSFP
HSVDSGRISPSHGFQRDLVRVIGNMCYQHFPNQEKVRELDGIPLLLDHCNIDDHNPYICQ
WAIFAIRNVLENNKENQDIVASIHPLGLADMSRLQQFGVDAVEFDGEKI
Now I want to find all duplicates in my big Fasta File and append numbers to the duplicates, so that I know which duplicate it is (1,2,3,...,x). When a new duplicate is found (one with another header), the counter should start from the beginning.
The output should be something like this:
>acrdi|AD19082
STSTAFPLLTQFYGCAIIILVLAMCCSCLVYAMYFMNSSGLQTHESTVTQKVKDFSLQ
WLQPILFGCSWRHRLIAKSRRNRSKIQPMTGTEPPWNESKDAFENLKTWALNKQNRNCLL
EINFLEAKDFIVMCKDVVCFEEDDKDERNLNLCLKTLTEAFRFLRNCCAETPKNQSFVIS
SGVAKQAIEVILILLRPVFQEREKGTEVITDTIRSGLQLLGNTVVKNIDTQEFIWNCCCP
QFFLDVLLSRHHSIQDCLCMIIFNCLNQQRRLQLVNNPKIISQIVHLCADKSLLEWGYFI
LDCLICEGLFPDLYQGMEFDPLARIILLDLFQVKITDALDESSERTERTETPKELYASSL
NYLAEQFETYFIDIIQRLQQLDYSSNDFFQVLVVTRLLSLLSTSTGLKSSMTGLQDRASL
LETCVDLLRETSKPEAKAAFKRPGTSYWEYVLPTFP
>acrdi|AD19082-1
MLRQSEPPWNESKDAFENLKTWALNKQNRNCLLEINFLEAKDFIVMCKDVVCFEEDDKDE
RNLNLCLKTLTEAFRFLRNCCAETPKNQSFVISSGVAKQAIEVILILLRPVFQEREKGTE
VITDTIRSGLQLLGNTVVKNIDTQEFIWNCCCPQFFLDVLLSRHHSIQDCLCMIIFNCLN
QQRRLQLVNNPKIISQIVHLCADKSLLEWGYFILDCLICEGLFPDLYQGMEFDPLARIIL
LDLFQVKITDALDESSERTERTETPKELYASSLNYLAEQFETYFIDIIQRLQQLDYSSND
FFQVLVVTRLLSLLSTSTGLKSSMTGLQDRASLLETCVDLLRETSKPEAKAAFSNVSSFP
HSVDSGRISPSHGFQRDLVRVIGNMCYQHFPNQEKVRELDGIPLLLDHCNIDDHNPYICQ
WAIFAIRNVLENNKENQDIVASIHPLGLADMSRLQQFGVDAVEFDGEKI
I would prefer a method with awk or sed, so that I can easily modify the code to run on all files in a directory.
I have to admit, that I am just starting to learn programming and parsing, but I hope this is not a stupid question.
THX in advance for the help.
An awk script:
BEGIN {
OFS="\n";
ORS=RS=">";
}
{
name = $1;
$1 = "";
suffix = names[name] ? "-" names[name] : "";
print name suffix $0, "\n";
names[name]++;
}
The above uses the ">" as a record separator, and checks the first field (which is the header name that can be duplicated). For each line it prints, it adds a suffix after the header name for each additional time the field appears (i.e. '-1' for the first dup, '-2' for the second...)
I wanted to remove duplicate lines from a file based on a column. A quick search let me this page which had the following solution:
awk '!x[$1]++' filename
It works, but I am not sure how it works. I know it uses associate arrays in awk but I am not able to infer anything beyond it.
Update:
Thanks everyone for the explanation. With my new knowledge, I have wrote a blog post with further explanation of how it works.
That awk script !x[$1]++ fills an array named x. Suppose the first word ($1 refers to the first word in a line of text) in a line of text is line1. It effectively results in this operation on the array:
x["line1"]++
The "index" (the key) of the array is the text encountered in the file (line1 in this example), and the value associated with that key is an integer that is incremented by 1.
When a unique line of text is encountered, the current value of the array is zero, which is then post-incremented to 1. The not operator ! evaluates to non-zero (true) for each new unique line of text and so prints it. The next time the same value is encountered, the value in the array is non-zero and so the not operation results in zero (false), so the line is not printed.
A less "clever" way of writing the same thing (but possibly more clear and less fun) would be this:
{
if (x[$1] == 0 )
print
x[$1]++
}