merge multiple fasta sequences in two files into a single file line by line

Question

[girijakaushal]

Hello,

I need to combine two fasta files having thousands of fasta sequences like:

File1:

>HWI-700823F:57:C97D4ANXX:8:1101:1295:2240 2:N:0:GTGAAACG
NAAGAGGGGAATCAGGAGGGACCGCAAATATGCAGTGCAGCCCCGTGCCGTGTATGCAAC
TGGGGTACACATGTCCCAGAACATAGCCGGGAAGTCAACG
>HWI-700823F:57:C97D4ANXX:8:1101:1587:2235 2:N:0:GTGAAACG
NTCTGCCGCTCTGCGTACAAGCTTGAGAGTTTTTTTGCAGACCTTCTTGCCGGCGAGAGG
CTTAGCTATGGGAGCCAAAGCCATCATCTTCTTCTTCTCT
>HWI-700823F:57:C97D4ANXX:8:1101:1974:2229 2:N:0:NTGAAANN
NCTAAGCATGCTTTGAACTTGATCTTCTCCTTCACGAATGGGAGCGATTGGGATGGTCCT
TACAGATTGCAGTTTCAAGTTCCCAAGGCTTGGCGAAACA

File2:

>HWI-700823F:57:C97D4ANXX:8:1101:1295:2240 1:N:0:GTGAAACG
GTCCCGTGATAATGGAAGTATTTGATTCTCTGCTCCGTCTTGTGCGTTGACTTCCCGGCT
ATGTTCTGGGACATGTGTACCCCAGTTGCATACACGGCAC
>HWI-700823F:57:C97D4ANXX:8:1101:1587:2235 1:N:0:GTGAAACG
CAGAAAGAGAAGAAGAAGATGATGGCTTTGGCTCCCATAGCTAAGCCTCTCGCCGGCAAG
AAGGTCTGCAAAAAAACTCTCAAGCTTGTACGCAGAGCGG
>HWI-700823F:57:C97D4ANXX:8:1101:1974:2229 1:N:0:NTGAAANN
CAACGATCGCCCCCTTCTGCAGACAAGTTACCAACCATGGCACAACTTGTGTCAACAATT
TGTGTGTCCGGAAAGATTGCTCTGTCACACGCGCCTTCT

I want to combine both files line by line and expected outcome is:

>HWI-700823F:57:C97D4ANXX:8:1101:1295:2240 2:N:0:GTGAAACG
NAAGAGGGGAATCAGGAGGGACCGCAAATATGCAGTGCAGCCCCGTGCCGTGTATGCAAC
TGGGGTACACATGTCCCAGAACATAGCCGGGAAGTCAACG
>HWI-700823F:57:C97D4ANXX:8:1101:1295:2240 1:N:0:GTGAAACG
GTCCCGTGATAATGGAAGTATTTGATTCTCTGCTCCGTCTTGTGCGTTGACTTCCCGGCT
ATGTTCTGGGACATGTGTACCCCAGTTGCATACACGGCAC
>HWI-700823F:57:C97D4ANXX:8:1101:1587:2235 2:N:0:GTGAAACG
NTCTGCCGCTCTGCGTACAAGCTTGAGAGTTTTTTTGCAGACCTTCTTGCCGGCGAGAGG
>HWI-700823F:57:C97D4ANXX:8:1101:1587:2235 1:N:0:GTGAAACG
CAGAAAGAGAAGAAGAAGATGATGGCTTTGGCTCCCATAGCTAAGCCTCTCGCCGGCAAG
AAGGTCTGCAAAAAAACTCTCAAGCTTGTACGCAGAGCGG

means, I want to combine both files like one sequence of 1st file then 1st sequence of 2nd file and so on.

I tried various commands but I am not able to parse this multiple fasta file, it takes 1st line as one sequence and not give desired output.

Please help me.

[girijakaushal]

Hi Pierre,

Should I firstly linerize my sequences and then use the paste and transform command? or this one line command is enough for getting desired output?

Thank you.

[GenoMax]

Please use ADD REPLY/ADD COMMENT to respond to existing posts.

Save following code in a file called linearize.awk

/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}

and then run the command as shown by @Pierre.

Answer 1

[Pierre Lindenbaum]

linearize , paste and transform:

paste <(awk -f linearize.awk file1.fa ) <(awk -f linearize.awk file2.fa  )| tr "\t" "\n"

[Pierre Lindenbaum]

opps , fixed paste at wrong position

Answer 2

[Medhat]

Using python / I did not test the code

from itertools import izip
file_1 = "path/to/file_1.fasta"
file_2 = "path/to/file_2.fasta"
with open("result.fasta", "w") as output, open(file_1, "r") as f_1,  open(file_2, "r") as f_2:
       for line_from_file_1, line_from_file_2 in izip(f_1, f_2):
              output.write("{}{}".format(line_from_file_1, f_1.next(),  line_from_file_2, f_2.next()))

Answer 3

[Matt Shirley]

[Medhat]

Thanks for this answer, It is much faster.

Answer 4

[Brian Bushnell]

You've got file 2 and file 1 mixed up, they should be swapped. File 1 should have headers like

HWI-700823F:57:C97D4ANXX:8:1101:1295:2240 1:N:0:GTGAAACG

Anyway, you can use the BBMap package's reformat tool like this:

reformat.sh in1=file.1fa in2=file2.fa out=interleaved.fa