This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Reformat my txt file

I have a txt file that looks like this:

A a,b,q
B d
D f,m

how can I convert it to:

A a
A b
A q
B d
D f
D m
rna-seq gene ontology
• 2,102 views • link
written by tianshenbio tianshenbio

1 answer

There are lots of ways, you should pick a language you would like to learn and then see if you can use it.

I picked Perl because the Python course was full.

This is 'command line' Perl which is really useful for this kind of simple parsing:

perl -ane '@s=split(/\,/, $F[1]); foreach $k (@s){print "$F[0] $k\n";}' txt.txt
• 0 views • link
written by bruce.moran bruce.moran

Hi,

Thank you for your reply. What if there is a space after each comma?

• 0 views • link
written by tianshenbio tianshenbio

Please let us know how this question is related to bioinformatics or the post will be closed.

• 0 views • link
written by Ram Ram

I think it's a toy example, and the A, B etc are indicative. User has some genuine bioinformatics q's.

Fair enough if you want to close it.

• 0 views • link
written by bruce.moran bruce.moran

I'm sure that is the case, but OP needs to add details on how this is related to bioinformatics for one simple reason - this might be a known or intermediate file format that others might encounter, and they may have the same question. Without context, there is no way they can locate this post and use your answer. In essence, OP's post as it is right now only has value to them and not to the community at large, and we do not encourage such posts.

• 0 views • link
written by Ram Ram

If you have this

A b, c, d, e
B f, g, h,

Then awk -F',| ' '{for (i=2;i<NF+1;i++){if (length($i) > 0){print $1,$i}}}' txt.txt

It even solves this:

A b,c, d,e,f, g,h, i, o
B h,d, y,u, i, o,
C h  f d,d g      k    l

Or even if you have multiple spaces or comas between two letters, it will have the same output.

• 0 views • link
updated by Ram Ram • written by Diedes • Diedes

Put a space after the comma in split: 

@s=split(/\,/, $F[1])

to

@s=split(/\, /, $F[1])
• 0 views • link
updated by Ram Ram • written by bruce.moran bruce.moran

Please do not answer questions that are unrelated to bioinformatics. We are not StackOverflow. If OP is not willing to show us how their question is related to bioinformatics, do not encourage them.

• 0 views • link
written by Ram Ram

Log in to answer this question.

More posts like this