How to split a column based on |?


 
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# 1  
Old 06-19-2017
How to split a column based on |?

Hi all,

Newbie here, so please bear over with my stupid question Smilie

I have used far too long time today on figuring this out, so I hope that someone here can help me move on.

I have some annotation data for a transcriptome where I want to split a column containing NCBI accession IDs into a column with GIs and REFs (I still want keep the rest of the columns - just split the IDs)

This is an example of a row in my data set:
Code:
TRINITY_DN17272_c0_g1_i1	gi|242003970|ref|XP_002422928.1|	57.5	127	54	0	2	382	65	191	1.2e-41	176.0

What I want:
Code:
TRINITY_DN17272_c0_g1_i1	242003970   XP_002422928.1   57.5	127	54	0	2	382	65	191	1.2e-41	176.0

I have tried the following:
Code:
cut -d'|' -f2,4 File.m8 | tr '|' '\t'

It splits perfectly - too perfectly because I loose everything else besides the two columns:
Code:
242003970   XP_002422928.1

Can someone please help me out?

Thanks! Birgitte
# 2  
Old 06-19-2017
Your target field separator is not clear - do you want the two elements to be each a field of its own with a <TAB> between them, or both making up one field, separated by a space or two?
For the first case, try
Code:
awk '{split ($2, T, "|"); $2 = T[2] OFS T[4]}1' OFS="\t" file
TRINITY_DN17272_c0_g1_i1    242003970    XP_002422928.1    57.5    127    54    0    2    382    65    191    1.2e-41    176.0


Last edited by RudiC; 06-19-2017 at 11:32 AM..
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# 3  
Old 06-19-2017
Code:
perl -pae '$F[1] = join "\t", (split /\|/, $F[1])[1,3] and $_ = join "\t", @F' BioBing.example

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# 4  
Old 06-19-2017
A less brute-force method:
Code:
tr '|' '\t' < infile > outfile

This User Gave Thanks to Corona688 For This Post:
# 5  
Old 06-19-2017
Quote:
Originally Posted by Corona688
A less brute-force method:
Code:
tr '|' '\t' < infile > outfile

Hi Corona688,

The OP requires more than just substituting every pipe symbol for a tab.
This User Gave Thanks to Aia For This Post:
# 6  
Old 06-19-2017
If you columns are fixed, then perhaps you could:-
Code:
tab=$(printf "\t")
tr '|' "$tab" < input_file | cut -d "$tab" -f1,3,5,7-

Does that help? What I'm trying is to convert every | to a tab and then cut the fields you want separating on a tab character. I hope it does what you wanted. I've set the variable tab just to make it clear. Feel free to replace it as it works best for you.




Kind regards,
Robin
This User Gave Thanks to rbatte1 For This Post:
# 7  
Old 06-20-2017
Quote:
Originally Posted by BioBing
Hi all,

Newbie here, so please bear over with my stupid question Smilie

I have used far too long time today on figuring this out, so I hope that someone here can help me move on.

I have some annotation data for a transcriptome where I want to split a column containing NCBI accession IDs into a column with GIs and REFs (I still want keep the rest of the columns - just split the IDs)

This is an example of a row in my data set:
Code:
TRINITY_DN17272_c0_g1_i1	gi|242003970|ref|XP_002422928.1|	57.5	127	54	0	2	382	65	191	1.2e-41	176.0

What I want:
Code:
TRINITY_DN17272_c0_g1_i1	242003970   XP_002422928.1   57.5	127	54	0	2	382	65	191	1.2e-41	176.0

I have tried the following:
Code:
cut -d'|' -f2,4 File.m8 | tr '|' '\t'

It splits perfectly - too perfectly because I loose everything else besides the two columns:
Code:
242003970   XP_002422928.1

Can someone please help me out?

Thanks! Birgitte
Since gi and ref seems to be always there, perhaps another suggestion:
Code:
perl -pe 's/\|?(?:\s+gi|ref)?\|\s*/\t/g' file

Output:
Code:
TRINITY_DN17272_c0_g1_i1        242003970       XP_002422928.1  57.5    127     54      02382     65      191     1.2e-41 176.0

This User Gave Thanks to Aia For This Post:
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