combine fasta sequences in combination from two different files

Question

[shome]

I have two files that look as follows:

file 1

>sp|P0|H1_HUMAN dhj OS=Homo sapiens OX=9606 GN=CDH1 PE=1 SV=3 
MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHLERGRVLGRVNFEDCTGRQRTAYFSLDTRFKVGTDGVITVKRPLRFHNPQIHFLVYAWDSTYRKFSTKVTLNTVG

>sp|Q4|C1_RAT C-1 jkjk OS=Rattus norvegicus OX=10116 GN=Cdh1 PE=1 SV=1 
QIKSNRDKETTVFYSITGPGADKPPVGVFIIERETGWLKVTQPLDREAIDKYLLYSHAVS

file 2

>sp|P641|A1_CHICK link OS=Gallus gallus OX=9031 GN=CDH1 PE=1 SV=2 

MGRRWGSPALQRFPVLVLLLLLQVCGRRCDEAAPCQPGFAAETFSFSVPQDSVAAGRELG

>sp|QF2|A2_BOVIN hjh OS=Bos taurus OX=9913 GN=CDH1 PE=2 SV=1 

MGPWSRSLSALCCCCRCNPWLCREPEPCIPGFGAESYTFTVPRRNLERGRVLGRVSFEGC

I am looking to combine all the fasta sequences from file1 with file2 and save it in new file output.fasta.

desired output file: output.fasta

 >sp|P0|H1_HUMAN dhj OS=Homo sapiens OX=9606 GN=CDH1 PE=1 SV=3_sp|P641|A1_CHICK link OS=Gallus gallus OX=9031 GN=CDH1 PE=1 SV=2
MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHLERGRVLGRVNFEDCTGRQRTAYFSLDTRFKVGTDGVITVKRPLRFHNPQIHFLVYAWDSTYRKFSTKVTLNTVGMGRRWGSPALQRFPVLVLLLLLQVCGRRCDEAAPCQPGFAAETFSFSVPQDSVAAGRELG
 >sp|P0|H1_HUMAN dhj OS=Homo sapiens OX=9606 GN=CDH1 PE=1 SV=3_>sp|QF2|A2_BOVIN hjh OS=Bos taurus OX=9913 GN=CDH1 PE=2 SV=1
MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHLERGRVLGRVNFEDCTGRQRTAYFSLDTRFKVGTDGVITVKRPLRFHNPQIHFLVYAWDSTYRKFSTKVTLNTVGMGPWSRSLSALCCCCRCNPWLCREPEPCIPGFGAESYTFTVPRRNLERGRVLGRVSFEGC
>sp|Q4|C1_RAT C-1 jkjk OS=Rattus norvegicus OX=10116 GN=Cdh1 PE=1 SV=1_>sp|P641|A1_CHICK link OS=Gallus gallus OX=9031 GN=CDH1 PE=1 SV=2
QIKSNRDKETTVFYSITGPGADKPPVGVFIIERETGWLKVTQPLDREAIDKYLLYSHAVSMGRRWGSPALQRFPVLVLLLLLQVCGRRCDEAAPCQPGFAAETFSFSVPQDSVAAGRELG
>sp|Q4|C1_RAT C-1 jkjk OS=Rattus norvegicus OX=10116 GN=Cdh1 PE=1 SV=1_>sp|QF2|A2_BOVIN hjh OS=Bos taurus OX=9913 GN=CDH1 PE=2 SV=1
QIKSNRDKETTVFYSITGPGADKPPVGVFIIERETGWLKVTQPLDREAIDKYLLYSHAVSMGPWSRSLSALCCCCRCNPWLCREPEPCIPGFGAESYTFTVPRRNLERGRVLGRVSFEGC

[Arup Ghosh]

Have you tried cat *.fasta > out.fasta?

how to combine multiple fasta file into a larger fasta file

[shome]

Hi Arup, Actually, I want to combine entry1 from file 1 with all possible entries of file2(and do the same for all entries of file) and save in output.fasta. Cat *.fasta will merge all fasta sequences no matter what...

[Ram]

You'll need to use custom BioPerl/BioPython code. What you are doing is not a standard operation. In fact, it is odd enough to warrant the question: What are you doing and why are you doing that?

[shome]

I need combined fasta sequences of entries from file 1 and file 2 to do a residue correlation analysis.Ok..I will check it out with biopython,but I thought it is possible with awk/unix..

[Ram]

Maybe with bioawk - but the operation is complicated enough to warrant a more robust, verifiable, reproducible approach, which one-liners are not.

[GenoMax]

sayaneshome.rsg : Take a look at seqkit (https://github.com/shenwei356/seqkit ). It may have an option (concat perhaps ) to do something like this.

Answer 1

[Pierre Lindenbaum]

assuming two lines per fasta record and no empty line.

cat input1.fa | paste  - - | while read L1; do cat input2.fa | paste - - | while read L2; do echo -e "$L1\t$L2" ; done ; done | awk -F '\t' '{printf("%s|%s\n%s%s\n",$1,substr($3,2),$2,$4);}'


>sp|P0|H1_HUMAN dhj OS=Homo sapiens OX=9606 GN=CDH1 PE=1 SV=3 |sp|P641|A1_CHICK link OS=Gallus gallus OX=9031 GN=CDH1 PE=1 SV=2 
MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHLERGRVLGRVNFEDCTGRQRTAYFSLDTRFKVGTDGVITVKRPLRFHNPQIHFLVYAWDSTYRKFSTKVTLNTVGMGRRWGSPALQRFPVLVLLLLLQVCGRRCDEAAPCQPGFAAETFSFSVPQDSVAAGRELG
>sp|P0|H1_HUMAN dhj OS=Homo sapiens OX=9606 GN=CDH1 PE=1 SV=3 |sp|QF2|A2_BOVIN hjh OS=Bos taurus OX=9913 GN=CDH1 PE=2 SV=1 
MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHLERGRVLGRVNFEDCTGRQRTAYFSLDTRFKVGTDGVITVKRPLRFHNPQIHFLVYAWDSTYRKFSTKVTLNTVGMGPWSRSLSALCCCCRCNPWLCREPEPCIPGFGAESYTFTVPRRNLERGRVLGRVSFEGC
>sp|Q4|C1_RAT C-1 jkjk OS=Rattus norvegicus OX=10116 GN=Cdh1 PE=1 SV=1 |sp|P641|A1_CHICK link OS=Gallus gallus OX=9031 GN=CDH1 PE=1 SV=2 
QIKSNRDKETTVFYSITGPGADKPPVGVFIIERETGWLKVTQPLDREAIDKYLLYSHAVSMGRRWGSPALQRFPVLVLLLLLQVCGRRCDEAAPCQPGFAAETFSFSVPQDSVAAGRELG
>sp|Q4|C1_RAT C-1 jkjk OS=Rattus norvegicus OX=10116 GN=Cdh1 PE=1 SV=1 |sp|QF2|A2_BOVIN hjh OS=Bos taurus OX=9913 GN=CDH1 PE=2 SV=1 
QIKSNRDKETTVFYSITGPGADKPPVGVFIIERETGWLKVTQPLDREAIDKYLLYSHAVSMGPWSRSLSALCCCCRCNPWLCREPEPCIPGFGAESYTFTVPRRNLERGRVLGRVSFEGC

[shome]

Hi @Pierre,is there anyway to do this if there are multiple lines per fasta record?

[GenoMax]

Linearize the fasta files. Courtesy of code from @Pierre:

Linearize a fasta sequence

awk -f linearizefasta.awk < input.fa

or

awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' < input.fa

Format back to fasta

tr "\t" "\n" < linearized.tsv

if you know your fasta header have a length < 60

tr "\t" "\n" < linearized.tsv | fold -w 60

view raw README.md hosted with ❤ by GitHub

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

view raw linearizefasta.awk hosted with ❤ by GitHub

[shome]

Thank you it worked based on your and Pierre's input.

[shome]

Hi If my fasta headers contain lines like this : >A0A2I3MB61_PAPAN/29-158; >A0A2IB61_HUMAN/29-10; how to only merge the fasta inputs where the string between _ and / matches. For instance, the fasta sequences only should combine if both are from human or from papan else wont..

[Ram]

I'll repeat my advice from before

You'll need to use custom BioPerl/BioPython code