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How to merge multiple .fasta flies retaining the file headers

Hi anyone has an idea about merging multiple .fasta flies retaining the file headers? I tried cat command but it will only keep the 1st header. What I want to do:

FileA

>Header1
Sequence1
>Header2
Sequence2

FileB

>Header3
Sequence3

FileC

>Header4
  Sequence4
>Header5
  Sequence5

What I want:

New File

>Header1
  Sequence1
>Header2
  Sequence2
>Header3
  Sequence3
>Header4
  Sequence4
>Header5
  Sequence5

Thank you so much for your help!

assembly sequencing
• 1,403 views • link
written by Azuretimes • Azuretimes

Why do you think cat doesn't work for this?

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written by Joe Joe

Hi Joe, I tried cat, but the problem is that it will only Header1 and lose other header information...

• 0 views • link
written by Azuretimes • Azuretimes

If you are using it correctly, as per genomax's answer, this cannot happen.

If it is the case, you're doing something else you aren't telling us.

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written by Joe Joe

Hi Joe, thanks for the reply. I followed genomax's answer and it worked finally,

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written by Azuretimes • Azuretimes

1 answer 

cat fileA fileB fileC > final_file
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written by GenoMax GenoMax

Hi, thanks for the reply. I tried cat, but the problem is that it will only Header1 and lose other header information..

• 0 views • link
written by Azuretimes • Azuretimes

No it won't. Not unless your files are made on some other OS and don't have correct unix endings. You should try to reformat your files using dos2unix command before cat.

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written by GenoMax GenoMax

Thanks for your suggestion! I tried dos2unix and it works!

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written by Azuretimes • Azuretimes

You can accept the answer "green checkmark" to provide closure to this thread.

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written by GenoMax GenoMax

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