CODEWITHSUNDEEP
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GKibet
GKibet

Reputation: 75

Sed/Awk: how to find and remove two lines if a pattern in the first line is being repeated; bash

I am processing text file(s) with thousands of records per file. Each record is made up of two lines: a header that starts with ">" and followed by a line with a long string of characters "-AGTCNR". The header has 10 fields separated by "|" whose first field is a unique identifier to each record e.g ">KEN096-15" and a record is termed duplicate if it has same identifier. Here is how a simple record look like:

>ACML500-12|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_-2  
----TAAGATTTTGACTTCTTCCCCCATCATCAAGAAGAATTGT-------  
>ACRJP458-10|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_N  
-----------TCCCTTTAATACTAGGAGCCCCTGACATAGCCTTTCCTAAATAAT-----  
>ASILO303-17|Dip|gs-Par|sp-Par vid|subsp-NA|co  
-------TAAGATTCTGATTACTCCCCCCCTCTCTAACTCTTCTTCTTCTATAGTAGATG  
>ASILO326-17|Dip|gs-Goe|sp-Goe par|subsp-NA|c  
TAAGATTTTGATTATTACCCCCTTCATTAACCAGGAACAGGATGA---------------  
>CLT100-09|Lep|gs-Col|sp-Col elg|subsp-NA|co-Buru  
AACATTATATTTGGAATTT-------GATCAGGAATAGTCGGAACTTCTCTGAA------  
>PMANL2431-12|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_  
----ATGCCTATTATAATTGGAGGATTTGGAAAACCTTTAATATT----CCGAAT  
>STBOD057-09|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_N  
ATCTAATATTGCACATAGAGGAACCTCNGTATTTTTTCTCTCCATCT------TTAG  
>TBBUT582-11|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_N  
-----CCCCCTCATTAACATTACTAAGTTGAAAATGGAGCAGGAACAGGATGA  
>TBBUT583-11|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_N  
TAAGATTTTGACTCATTAA----------------AATGGAGCAGGAACAGGATGA  
>AFBTB001-09|Col|gs-NA|sp-NA|subsp-NA|co-Ethi|site-NA|lat_N  
TAAGCTCCATCC-------------TAGAAAGAGGGG---------GGGTGA  
>PMANL2431-12|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_  
----ATGCCTATTAGGAAATTGATTAGTACCTTTAATATT----CCGAAT---  
>AFBTB003-09|Col|gs-NA|sp-NA|subsp-NA|co-Ethi|site-NA|lat_N  
TAAGATTTTGACTTCTGC------CATGAGAAAGA-------------AGGGTGA  
>AFBTB002-09|Cole|gs-NA|sp-NA|subsp-NA|co-Ethi|site-NA|lat_N  
-------TCTTCTGCTCAT-------GGGGCAGGAACAGGG----------TGA  
>ACRJP458-10|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_N  
-----------TCCCTTTAATACTAGGAGCCCCTTTCCT----TAAATAAT-----

Now I am triying to delete repeats, like duplicate records of "ACRJP458-10" and "PMANL2431-12". Using a bash script I have extracted the unique identifiers and stored repeated ones in a variable "$duplicate_headers". Currently, I am trying to find any repeated instances of their two-line records and deleting them as follows:

for i in "$@"
do
    unset duplicate_headers
    duplicate_headers=`grep ">" $1 | awk 'BEGIN { FS="|"}; {print $1 "\n"; }' | sort | uniq -d`
    for header in `echo -e "${duplicate_headers}"`
    do
        sed -i "/^.*\b${header}\b.*$/,+1 2d" $i
        #sed -i "s/^.*\b${header}\b.*$//,+1 2g" $i
        #sed -i "/^.*\b${header}\b.*$/{$!N; s/.*//2g; }" $i
    done
done

The final result (with thousands of records in mind) will look like:

>ACML500-12|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_-2  
----TAAGATTTTGACTTCTTCCCCCATCATCAAGAAGAATTGT-------  
>ACRJP458-10|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_N  
-----------TCCCTTTAATACTAGGAGCCCCTGACATAGCCTTTCCTAAATAAT-----  
>ASILO303-17|Dip|gs-Par|sp-Par vid|subsp-NA|co  
-------TAAGATTCTGATTACTCCCCCCCTCTCTAACTCTTCTTCTTCTATAGTAGATG  
>ASILO326-17|Dip|gs-Goe|sp-Goe par|subsp-NA|c  
TAAGATTTTGATTATTACCCCCTTCATTAACCAGGAACAGGATGA---------------  
>CLT100-09|Lep|gs-Col|sp-Col elg|subsp-NA|co-Buru  
AACATTATATTTGGAATTT-------GATCAGGAATAGTCGGAACTTCTCTGAA------  
>PMANL2431-12|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_  
----ATGCCTATTATAATTGGAGGATTTGGAAAACCTTTAATATT----CCGAAT  
>STBOD057-09|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_N  
ATCTAATATTGCACATAGAGGAACCTCNGTATTTTTTCTCTCCATCT------TTAG  
>TBBUT582-11|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_N  
-----CCCCCTCATTAACATTACTAAGTTGAAAATGGAGCAGGAACAGGATGA  
>TBBUT583-11|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_N  
TAAGATTTTGACTCATTAA----------------AATGGAGCAGGAACAGGATGA  
>AFBTB001-09|Col|gs-NA|sp-NA|subsp-NA|co-Ethi|site-NA|lat_N  
TAAGCTCCATCC-------------TAGAAAGAGGGG---------GGGTGA  
>AFBTB003-09|Col|gs-NA|sp-NA|subsp-NA|co-Ethi|site-NA|lat_N  
TAAGATTTTGACTTCTGC------CATGAGAAAGA-------------AGGGTGA  
>AFBTB002-09|Cole|gs-NA|sp-NA|subsp-NA|co-Ethi|site-NA|lat_N  
-------TCTTCTGCTCAT-------GGGGCAGGAACAGGG----------TGA

Upvotes: 2

Views: 74

Answers (1)

Ed Morton
Ed Morton

Reputation: 203493

$ awk -F'[|]' 'NR%2{f=seen[$1]++} !f' file
>ACML500-12|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_-2
----TAAGATTTTGACTTCTTCCCCCATCATCAAGAAGAATTGT-------
>ACRJP458-10|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_N
-----------TCCCTTTAATACTAGGAGCCCCTGACATAGCCTTTCCTAAATAAT-----
>ASILO303-17|Dip|gs-Par|sp-Par vid|subsp-NA|co
-------TAAGATTCTGATTACTCCCCCCCTCTCTAACTCTTCTTCTTCTATAGTAGATG
>ASILO326-17|Dip|gs-Goe|sp-Goe par|subsp-NA|c
TAAGATTTTGATTATTACCCCCTTCATTAACCAGGAACAGGATGA---------------
>CLT100-09|Lep|gs-Col|sp-Col elg|subsp-NA|co-Buru
AACATTATATTTGGAATTT-------GATCAGGAATAGTCGGAACTTCTCTGAA------
>PMANL2431-12|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_
----ATGCCTATTATAATTGGAGGATTTGGAAAACCTTTAATATT----CCGAAT
>STBOD057-09|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_N
ATCTAATATTGCACATAGAGGAACCTCNGTATTTTTTCTCTCCATCT------TTAG
>TBBUT582-11|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_N
-----CCCCCTCATTAACATTACTAAGTTGAAAATGGAGCAGGAACAGGATGA
>TBBUT583-11|Lep|gs-NA|sp-NA|subsp-NA|co-Buru|site-NA|lat_N
TAAGATTTTGACTCATTAA----------------AATGGAGCAGGAACAGGATGA
>AFBTB001-09|Col|gs-NA|sp-NA|subsp-NA|co-Ethi|site-NA|lat_N
TAAGCTCCATCC-------------TAGAAAGAGGGG---------GGGTGA
>AFBTB003-09|Col|gs-NA|sp-NA|subsp-NA|co-Ethi|site-NA|lat_N
TAAGATTTTGACTTCTGC------CATGAGAAAGA-------------AGGGTGA
>AFBTB002-09|Cole|gs-NA|sp-NA|subsp-NA|co-Ethi|site-NA|lat_N
-------TCTTCTGCTCAT-------GGGGCAGGAACAGGG----------TGA

To run it on multiple files at once would be this to remove duplicates across all files:

awk -F'[|]' 'FNR%2{f=seen[$1]++} !f' *

or this to only remove duplicates within each file:

awk -F'[|]' 'FNR==1{delete seen} FNR%2{f=seen[$1]++} !f' *

Upvotes: 3

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