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843
Posted By newbie83
Join multiple files with filename
Please help, I want to join multiple files based on column 1, and put the missing values as 0. Also the colname in the output should say which file the values came from.

FILE1
1 11
2 12
3 13
...
5,698
Posted By newbie83
fantastic, works , thank you so much !! ...
fantastic, works , thank you so much !!


Hi Don,

I tested with small samples and everything seems to work, I was wondering about the run-time of the original data.
File1 is 3.5Mb and File2 is...
5,698
Posted By newbie83
Thank you for being so patient, here is the...
Thank you for being so patient, here is the information you requested. the code still doesnt produce output, it is the same as file1


od -c inp2.txt
0000000 Q 0 U R 5 1 \t Q 0 ...
5,698
Posted By newbie83
I have made up an output manually if that helps
I have made up an output manually if that helps
5,698
Posted By newbie83
111065707: 169605479 is supposed to be the 5th...
111065707: 169605479 is supposed to be the 5th column in the input file2, I need to search 169605479 from file1 in the 5th column, which is present as a sub-field separated by ':' , I can see there...
5,698
Posted By newbie83
I`m terribly sorry for the confusion, the output...
I`m terribly sorry for the confusion, the output should be the following with only line1 col2 in file1 being found in file2, the rest of the lines appear in the same way as file1.

First line of...
5,698
Posted By newbie83
Thanks, but it is not producing any output, what...
Thanks, but it is not producing any output, what am I doing wrong? I changed $4 to $5, added a new field to dataset

# cat > inp2.txt
Q0UR51 Q0UR51_PHANO 5973037 XP_001796160.1 111065707:...
5,698
Posted By newbie83
Can you let me know what I`m doing wrong, this is...
Can you let me know what I`m doing wrong, this is part of a real data-set where I`m trying to search col2 from file1 in col5 in file2.

File2
# cat inp2.txt
Q0UR51 Q0UR51_PHANO 5973037...
5,698
Posted By newbie83
is it possible to limit the search by the first...
is it possible to limit the search by the first hit? That will reduce the runtime considerably, so as soon as the first hit is met, I would like to move on to the next line in file1, similar to a...
5,698
Posted By newbie83
Grepping one file column from another file
Hi all,

I want to search the second col of a file as a sub-part of 4th col of another file and produce a joint output. In the example, search if B is contained as a sub-part in E:B:C (sub-parts...
4,975
Posted By newbie83
This is easily done with the package bedtools...
This is easily done with the package bedtools with FastaFromBed function

https://code.google.com/p/bedtools/

# cat input1.fasta
>P02649...
1,489
Posted By newbie83
No, I have copied and pasted your code, I have...
No, I have copied and pasted your code, I have Linux, awk usually worked file until now.. let me try in another machine

---------- Post updated at 03:31 PM ---------- Previous update was at 03:17...
1,489
Posted By newbie83
Strange indeed !! # cat file1.txt [OR]...
Strange indeed !!

# cat file1.txt
[OR] KOG0001 Ubiquitin and ubiquitin-like proteins
ath: At1g31340
ath: At1g53930
ath: At1g53950
[J] KOG0002 60s ribosomal protein L39
ath: ...
1,489
Posted By newbie83
This doesn't produce any output, even with the...
This doesn't produce any output, even with the sample data.
1,489
Posted By newbie83
Connecting 3 files
Hi,

I`m trying to do functional categorization of a species and I need to join 3 files for that. I want to look up the code for each record in file 3 in file 1 ,
code indicated within brackets[]...
5,446
Posted By newbie83
Looping through files in pairs
Hi all,

Please guide. It has to do with parsing the input file names.

I have a fairly large number of files, I want to do some operations on them in a pairwise fashion (every file has a pair)....
1,195
Posted By newbie83
Work on multiple directories, same filename
Can this be done and if yes how?
I have 10 directories that end with the name 'cuff'

eg dir1-cuff , dir2-cuff

All these directories have a file named xyz.gtf


How do I run the same code...
1,299
Posted By newbie83
grep Fax your_file > tmp awk '{ gsub(/Fax:/,...
grep Fax your_file > tmp
awk '{ gsub(/Fax:/, ""); print $0}' tmp
1,404
Posted By newbie83
Please help the code is not appropriately...
Please help

the code is not appropriately work for the second awk, first example runs just fine...Also I need to condition on the term "collect" win col1 which is missing from the code..Since I...
2,495
Posted By newbie83
Loop through directory names
Some guidance is highly appreciated.

I have 10 directories with names ending with 'xyz', each of them have about 30000 files. I want to loop through the contents of each directory and produce a...
1,404
Posted By newbie83
Scrutinizer I get the same..got the collect...
Scrutinizer I get the same..got the collect within '' previously..sorry about that

Now for the second step I can do this for getting same rows together..but values will repeat...how do I get them...
1,404
Posted By newbie83
thank you for helping me learn, I will ask again...
thank you for helping me learn, I will ask again if I have issues..

---------- Post updated at 01:38 AM ---------- Previous update was at 01:29 AM ----------

krishmaths, your code uses just 2...
1,404
Posted By newbie83
Get value from column subsection
Please help me with this, I want to collect unique tbc values present in the
2nd col when the 1st col says 'collect' ..Order does not matter.. 2nd col is sub sectioned by ; and tb code values are in...
2,966
Posted By newbie83
Print rows with substring in column
Hi I want to print all rows where there is the alphabet N in the 6th column as a substring.

Here is what i tried and not working.Please help !


awk ' { if ( $6 == *"N"* ) print $0} '
...
2,839
Posted By newbie83
Plot python script output to file
Hi all,

I`m trying to generate some plots using a python package named splicegrapher.
I have access to a cluster which does not allow X11 forwarding and as a result I get RuntimeError: could not...
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