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Remove Duplicate Two Line Pairs?

 
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# 1  
Old 02-25-2013
Remove Duplicate Two Line Pairs?
So I have a bunch of files that look like this
Code:
>gi|33332323
MMKCRGVIMVVEKVMKRDGRIVPFDESRIRWAVQ---
>gi|45235353
MMKCR----VEKMRDVFFDESIRWAVQ

They go on...sequences are much longer but all in two line (fasta) format.

I want to remove duplicate pairs of ID(GI) number and sequence. I tried using grep ">" to get all the header lines, then sort -u > uniquegilist. Then I wrote the loop
Code:
for x in `cat uniquegilist`; do grep -m 1 -A1 $x sequencefile;done

I'm not sure why it didn't work, but that just returned the list of unique GI numbers and didn't include the sequences.

Any ideas on how to grab the unique GI # and sequence together...preferably preserving format?
# 2  
Old 02-25-2013
Code:
paste - - < uniquegilist | awk '!a[$0]++' | tr '\t' '\n'

# 3  
Old 02-25-2013
This still only returns the list of unique gi numbers, not their respective sequences.
# 4  
Old 02-25-2013
This is what I get:

1. Created a file with duplicate number and sequence:
Code:
$ cat uniquegilist
>gi|33332323
MMKCRGVIMVVEKVMKRDGRIVPFDESRIRWAVQ---
>gi|45235353
MMKCR----VEKMRDVFFDESIRWAVQ
>gi|33332323
MMKCRGVIMVVEKVMKRDGRIVPFDESRIRWAVQ---

2. This is the output when running the command:
Code:
$ paste - - < uniquegilist | awk '!a[$0]++' | tr '\t' '\n'
>gi|33332323
MMKCRGVIMVVEKVMKRDGRIVPFDESRIRWAVQ---
>gi|45235353
MMKCR----VEKMRDVFFDESIRWAVQ

Is the content of your file in same format? Number in one line followed by sequence in another?
# 5  
Old 02-25-2013
oh this does work! I made a mistake entering it. Thanks so much!

---------- Post updated at 10:31 PM ---------- Previous update was at 10:28 PM ----------

It seems that this removes some duplicates but not all. I still have entries with the same GI and same sequence.
# 6  
Old 02-25-2013
May be there are extra blank spaces, try this code:
Code:
paste - - < uniquegilist | awk '{$1=$1}1' | awk '!a[$0]++' | tr ' ' '\n'

# 7  
Old 02-25-2013
Doesn't do it unfortunately.
 
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