extract several fasta file with a list of ID (in order)

Question

[Chvatil]

I have a file with several names such :

seq1 seq9 seq3 seq7 seq5 seqi seqn....

and another fasta file with all my sequences, and what I need to do is to order my sequences by the order of the list above:such as:

>seq1
aaaaa
>seq9
aaaaa
>seq3
aaaaa
>seq7
aaaaa
>seq5
aaaaa
...

I tried this:

input_file = open('concatenate_0035_0042_aa2.fa','r')
output_file = open('result.fasta','a')


liste=['seq1','seq5','seq8' etc]
print(len(liste))
compteur=1
for i in liste:
    record_dict = SeqIO.to_dict(SeqIO.parse("concatenate_0035_0042_aa2.fa", "fasta"))
    print(">",record_dict[i].id,file=output_file,sep="")
    print(record_dict[i].seq,file=output_file)
    compteur+=1
    print(compteur)

output_file.close()
input_file.close()

but it actually takes too much time.

[h.mon]

There is a big number of solutions, and as Pierre said, an even bigger number of previous posts with the same question. You may use samtools faidx, as per my answer here.

[Chvatil]

Thanks you for you help.

[Pierre Lindenbaum]

this question has been asked a large number of times here. Please search for this question. Nevertheless, regarding your code, instead of doing your loop liste-nth times. How about scanning the fasta only one time and check if the current fasta name is in your liste ?

[Chvatil]

Ok, thanks you, now it work :)

input_file = open('concatenate_0035_0042_aa2.fa','r') output_file = open('result.fasta','a')

compteur=1
record_dict = SeqIO.to_dict(SeqIO.parse("concatenate_0035_0042_aa2.fa", "fasta"))
for i in liste:
    if i in record_dict:
        print(">",record_dict[i].id,file=output_file,sep="")
        print(record_dict[i].seq,file=output_file)

output_file.close()
input_file.close()