UNIX for Dummies Questions & Answers

Hi

I have a txt file with 4 columns where I need to add 4 empty columns in the middle meaning that I need what is currently column 4 to be column 8 in a new file.

The idea is that I have to use the file as input in a program that reads the data in column 1 and 8, so the content of the other columns doesn't matter.

I am a total newbie but have tried something like:

gawk '{print $1,"\t ","\t ","\t ","\t " , $2 , $3 , $4}' filename.txt > test

And this adds space between the original columns 1 and 2 but apparently this doesn't qualify as being columns but just "space".

I keep getting the following error when running my program(and there's nothing wrong with that command because it works with a file with the correct number of columns):

READING HLA POPULATION COVERAGE FILE:test
Traceback (most recent call last):
File "/home/people/lunde/python/popcover6_HLAonly.py", line 349, in ?
HLAcoverindex, popcoverlist = readpop(open(opts.coveragefilename, 'r'))
File "/home/people/lunde/python/popcover6_HLAonly.py", line 105, in readpop
coverage = float(fields[7])
IndexError: list index out of range

Hope someone can help me out. Please!

Can you post a small sample of the input file?

something like the results of

Code:

cat -vet filename.txt | head

This is the input file where the current column 4 needs to become column 8:

cat -vet Nordirland_alleler.tab.txt | head

A*0201^IIreland Northern^I46.8^I0.274^I^I^I^I^I$
A*0101^IIreland Northern^I36.4^I0.202^I^I^I^I^I$
A*0301^IIreland Northern^I26.3^I0.143^I^I^I^I^I$
A*1101^IIreland Northern^I15.0^I0.080^I^I^I^I^I$
A*24020101^IIreland Northern^I12.0^I0.061^I^I^I^I^I$
A*2902^IIreland Northern^I9.5^I0.049^I^I^I^I^I$
A*3201^IIreland Northern^I6.1^I0.032^I^I^I^I^I$
A*310102^IIreland Northern^I5.1^I0.026^I^I^I^I^I$
A*2501^IIreland Northern^I3.9^I0.020^I^I^I^I^I$
A*680102^IIreland Northern^I3.9^I0.020^I^I^I^I^I$

Is the fieldseparator a "^" sign? Better is to post your input file and the desired output.

Regards

See here's the problem with being a total newbie - don't know what defines the fieldseperator.
I just now that the ^| indicates tabs and the $ is the end-of-line-indicator or something like that. Never used -vet with cat before so only just found that out this morning. :-)

But the input file is saved as tab-delimited txt from an excel file meaning I have four columns like:

A*0201 Ireland Northern 46.8 0.274
A*0101 Ireland Northern 36.4 0.202

and I wan't

A*0201 Ireland Northern 46.8 xx xx xx xx 0.274
A*0101 Ireland Northern 36.4 xx xx xx xx 0.202

The position and content of the extra four columns(or the middle 6 columns) doesn't matter - I just need to create a Tab-delimited txt-file with A*0201 in column 1 and 0.274 in column 8.
I could start from the beginning and add the extra columns in the original excel file but I wan't to know how to do it using only Unix.

Really want to learn this but have zero experience with programming of any kind....

You may try with empty fileds (use nawk or /usr/xpg4/bin/awk on Solairs):

Or:

Code:

awk -F'\t' '$NF="x\tx\tx\tx\t"$NF' OFS='\t' infile

How cool was that!! It worked! Thanks!

Used this command:

gawk -F'\t' '{$8=$4;$4=_ }1' OFS='\t' myfile > Newfile

And got the desired output which my program reads as it should:
A*0201 Ireland Northern 46.8 0.274
A*0101 Ireland Northern 36.4 0.202
A*0301 Ireland Northern 26.3 0.143

But well I would like to understand it so that I would be able to use it sometime in a different but similar problem.

So if the -F'\t' part defines the fieldseperator what does the OFS='\t' part do and why is it necessary with both parts?

And what does the ;$4=_)1 part of the command do?