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Filling a tab-separated file with known missing entries in columns

 
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# 1  
Old 04-10-2012
Filling a tab-separated file with known missing entries in columns
Hello all,

I have a file which is tab separated like that:


Code:
PHE_205_A    TIP_127_W    ARG_150_B
MET_1150_A    TIP_12_W    VAL_11_B
GLU_60_A    TIP_130_W    ARG_143_B
LEU_1033_A    TIP_203_W    ARG_14_B
SER_1092_A    TIP_203_W    
THR_1090_A    TIP_203_W    
SER_1092_A    TIP_25_W    SER_104_B
TYR_15_B    TIP_25_W    
ASP_61_A    TIP_34_W    THR_134_B
SER_1204_A    TIP_46_W    ASP_8_B
ASP_61_A    TIP_63_W    ARG_131_B
THR_90_A    TIP_76_W    TYR_49_B
THR_1090_A    TIP_91_W    SER_100_B


and I want it to be like that:
Code:
PHE_205_A    TIP_127_W    ARG_150_B
MET_1150_A    TIP_12_W    VAL_11_B
GLU_60_A    TIP_130_W    ARG_143_B
LEU_1033_A    TIP_203_W    ARG_14_B
SER_1092_A    TIP_203_W    ARG_14_B
THR_1090_A    TIP_203_W    ARG_14_B
SER_1092_A    TIP_25_W    SER_104_B
SER_1092_A    TIP_25_W    TYR_15_B   
ASP_61_A    TIP_34_W    THR_134_B
SER_1204_A    TIP_46_W    ASP_8_B
ASP_61_A    TIP_63_W    ARG_131_B
THR_90_A    TIP_76_W    TYR_49_B
THR_1090_A    TIP_91_W    SER_100_B

The missing entry is always the one found in the line before it (if it is _B, then it is always _B, similar is for _A)

I would really appreciate if somebody would give me an idea on how to re-format it....

Thanks!

Moderator's Comments:
Mod Comment Please use code tags instead of quote tags (one button to the right)
Last edited by Scrutinizer; 04-10-2012 at 11:00 AM..
# 2  
Old 04-10-2012
Try
Code:
awk '
NF == 3 { f = $3 }
NF == 2 { $3 = f }
1' FILE

# 3  
Old 04-10-2012
Quote:
Originally Posted by yazu
Try
Code:
awk '
NF == 3 { f = $3 }
NF == 2 { $3 = f }
1' FILE

this code is doing the job well for the third column, but is screwing the first one...
output:

Code:
PHE_205_A    TIP_127_W    ARG_150_B
MET_1150_A    TIP_12_W    VAL_11_B
GLU_60_A    TIP_130_W    ARG_143_B
LEU_1033_A    TIP_203_W    ARG_14_B
SER_1092_A    TIP_203_W    ARG_14_B
THR_1090_A    TIP_203_W    ARG_14_B
SER_1092_A    TIP_25_W    SER_104_B
TYR_15_B    TIP_25_W    SER_104_B
ASP_61_A    TIP_34_W    THR_134_B
SER_1204_A    TIP_46_W    ASP_8_B
ASP_61_A    TIP_63_W    ARG_131_B
THR_90_A    TIP_76_W    TYR_49_B
THR_1090_A    TIP_91_W    SER_100_B

what is wrong is the bold entry, where SER_1092_A should be....
to exlpain, the output of this line should be

SER_1092_A TIP_25_W TYR_15_B
*Always *_A should be in the first column, TIP* in the second and *_B in the third....
Last edited by Scrutinizer; 04-10-2012 at 11:00 AM..
# 4  
Old 04-10-2012
Oh... Well, I didn't notice. But I think it's impossible without additional information - how should the program determine what field is absent? Is the second field always present and it is TIPxxx?
# 5  
Old 04-10-2012
Yes, in the second field TIP is there.

if a field is absent, either entries ending in _A or in _B will be missing.

So the program can read the line with the missing information (has two columns only):
-If it misses entry _B,
then it can go to the previous line,
find the _B entry and copy it in the third column.
Else if it misses _A,
go to the previous line,
find the _A entry and copy it in the first field and then swap TIP column and *_B
so that always the three column format should be *_A TIP* *_B

That's the idea.....

Thanks a lot!
# 6  
Old 04-10-2012
Use three Array elements to hold on to the last A,B or W value. The part after the last _ is the designator. Empty fields get stored in a 4th element array[" "], that never gets printed.. Try something like this..
Code:
awk -F'\t' '{for(i=1;i<=NF;i++){c=$i; sub(/.*_/,x,c); P[c]=$i} print P["A"],P["W"],P["B"]}' OFS='\t' infile

Output:
Code:
PHE_205_A	TIP_127_W	ARG_150_B
MET_1150_A	TIP_12_W	VAL_11_B
GLU_60_A	TIP_130_W	ARG_143_B
LEU_1033_A	TIP_203_W	ARG_14_B
SER_1092_A	TIP_203_W	ARG_14_B
THR_1090_A	TIP_203_W	ARG_14_B
SER_1092_A	TIP_25_W	SER_104_B
SER_1092_A	TIP_25_W	TYR_15_B
ASP_61_A	TIP_34_W	THR_134_B
SER_1204_A	TIP_46_W	ASP_8_B
ASP_61_A	TIP_63_W	ARG_131_B
THR_90_A	TIP_76_W	TYR_49_B
THR_1090_A	TIP_91_W	SER_100_B

Last edited by Scrutinizer; 04-10-2012 at 11:49 AM..
This User Gave Thanks to Scrutinizer For This Post:
TheTransporter
# 7  
Old 04-10-2012
the code is functional and extremely fast! Although I get the idea, still I couldn't write it! Will look into it.

Thanks Scrutinizer.
 
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