How to remove duplicate sequences in fasta file using python?

Question

[horsedog]

I have a two fasta files, file 1 and file 2 ,they have a lot of overlapped sequences but not all of them, here I want to merge these two files into one file file 3 and remove the duplicate part, just keeping the unique one, is there code example for python use? Well the duplicate here means the exact same query name and sequences, like these two:

>YP_204112.2
MEHYISLLVKSIFIENMALSFFLGMCTFLAVSKKVKTSFGLGVAVVVVLTIAVPVNNLVYTYLLKENALV
AGVDLTFLSFITFIGVIAALVQILEMILDRFFPPLYNALGIFLPLITVNCAIFGGVSFMVQRDYNFAESV
VYGFGSGIGWMLAIVALAGIREKMKYSDVPPGLRGLGITFITVGLMALGFMSFSGVQL

>YP_204112.2
MEHYISLLVKSIFIENMALSFFLGMCTFLAVSKKVKTSFGLGVAVVVVLTIAVPVNNLVYTYLLKENALV
AGVDLTFLSFITFIGVIAALVQILEMILDRFFPPLYNALGIFLPLITVNCAIFGGVSFMVQRDYNFAESV
VYGFGSGIGWMLAIVALAGIREKMKYSDVPPGLRGLGITFITVGLMALGFMSFSGVQL

Many thanks!

[GenoMax]

Is there a reason you seem to want a python solution everytime? CD-HIT is meant for this sort of application.

[horsedog]

Well thank you very much! I'll take a look into CDHIT! no reason just I'm practising python recently so I would like to see how people solve problem by python.

Answer 1

[Alex Reynolds]

Shorter option via awk:

$ cat one.fa two.fa | awk -vRS=">" '!a[$0]++ { print ">"$0; }' - > answer.fa

If you want to replicate this with Python, you could look at using a dictionary to store unique keys.

[horsedog]

hi , it said "invalid -v"

[Alex Reynolds]

Are you using GNU awk? If you're using OS X, install GNU awk via Homebrew: brew install gawk

[horsedog]

Hi again, well you're right it works now, but it's so weird cuz in the "answer.fa" it contains even more lines than file1 plus file2, which means that seems it didn't 'remove' but 'add'? (I used wc -l to count lines)

[Alex Reynolds]

Maybe grab the first few lines of both files and try it out on those test files. I'm not sure why you get that result; this is a pretty common use of awk.

[souzademedeiros]

I like the simplicity! This method almost worked for me, but was printing empty lines and one line with only '>'. I'm not an expert in awk, so filtering results by using grep:

cat one.fa two.fa | awk -v RS=">" '!a[$0]++ { print ">"$0; }' - | grep -Ev '^\s*$|^>\s*$' > answer.fa

Answer 2

[tiago211287]

This task can be accomplished with FASTA/Q Collapser quickly.

Answer 3

[lakhujanivijay]

One liner using seqkit

zcat fasta.fa.gz | seqkit rmdup -s -i -m -o clean.fa.gz -d duplicated.fa.gz -D duplicated.detail.txt

• Documents: http://bioinf.shenwei.me/seqkit (Usage, FAQ, Tutorial, Benchmark and Development Notes)
• Source code: https://github.com/shenwei356/seqkit

[gildas.lepennetier]

Fast and do the job nicely. The inspection of the duplicated is very helpful. Best option for me so far.

Answer 4

[michau]

Learn to use Biopython library. It's handy as hell. You can use any format as in/out

from Bio import SeqIO

with open('output.fasta', 'a') as outFile:
    record_ids = list()
    for record in SeqIO.parse('input.fasta', 'fasta'):
        if record.id not in record_ids:
            record_ids.append( record.id)
            SeqIO.write(record, outFile, 'fasta')

[Joe]

It should be noted this only checks for duplicates based on their IDs, which is not always going to be the most robust way to do it. It would probably be best to check for duplicated sequences which is what most of the other solutions are doing.

Answer 5

[pauley-p]

This is a python based alternative to your issue that uses BioPy

https://github.com/MJChimal/BiologPy/blob/master/drop_unique_records.py

Hope it still helps! :)

Answer 6

[shoujun.gu]

This python code will combine all the input fasta files (any number of files), and output 1 file with duplicated sequences removed. Note: if your input fasta files are too big to load into memory, this code will fail.

input_files=[list of input file names]
output_file='output_file_name'

holder=[]
for file in input_files:
    with open(file,'r') as file:
        rec=file.read().split('>')[1:]
        rec=['>'+i.strip()+'\n' for i in rec]
    holder.extend(rec)

total='\n'.join(list(set(holder)))

with open(output_file,'w') as out:
    out.write(total)