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People here won't know what fasta is

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edited Aug 4, 2019 at 17:28

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I have multiple .fastatext files such as:

file1:

>ID_000_FLNNKGHD_01376 
-ATGAATACAGAGGAAAAAACACCGCTTGCATACAAT
>ID_000_MGCDKLCO_02388 
ATGAAGGTGGAAAAAACACCGCTTGCATTT
>ID_000_OMAMOGKP_02746
--ATGTTGGTGGAAAAAACACCGCTTGCGGTA

file2:

>ID_000_KGHDAAD_06245 
AAATACAGAGGAAAAAACACCGCTTGCATACAAT
>ID_000_KOAAFG_40481 
CCCCAGGAAGGTGGAAAAAACACCGCTTGCAAA
>ID_000_GPAAAGVV_07764
--AAATTGGTGG---------ACACCGCTTTT--

etc.

I need to concatenate the first and second lines, third and fourth lines, etc. of each file and output a new file for each result like this:

file1 output:

>ID_000_FLNNKGHD_01376-ID_000_KGHDAAD_06245 
-ATGAATACAGAGGAAAAAACACCGCTTGCATACAATAAATACAGAGGAAAAAACACCGCTTGCATACAAT

file2 output:

>ID_000_MGCDKLCO_02388-ID_000_KOAAFG_40481
ATGAAGGTGGAAAAAACACCGCTTGCATTTCCCCAGGAAGGTGGAAAAAACACCGCTTGCAAA

file3 output:

>ID_000_OMAMOGKP_02746-ID_000_GPAAAGVV_07764
--ATGTTGGTGGAAAAAACACCGCTTGCGGTA--AAATTGGTGG---------ACACCGCTTTT--

etc.

*note that the first line needs to start with ">" and is concatanated putting a "-" between each string, and the second line is just put together

outputs needs to be named file_1.fasta to file_n.fasta

Thanks!

I have multiple .fasta files such as:

file1:

>ID_000_FLNNKGHD_01376 
-ATGAATACAGAGGAAAAAACACCGCTTGCATACAAT
>ID_000_MGCDKLCO_02388 
ATGAAGGTGGAAAAAACACCGCTTGCATTT
>ID_000_OMAMOGKP_02746
--ATGTTGGTGGAAAAAACACCGCTTGCGGTA

file2:

>ID_000_KGHDAAD_06245 
AAATACAGAGGAAAAAACACCGCTTGCATACAAT
>ID_000_KOAAFG_40481 
CCCCAGGAAGGTGGAAAAAACACCGCTTGCAAA
>ID_000_GPAAAGVV_07764
--AAATTGGTGG---------ACACCGCTTTT--

etc.

I need to concatenate the first and second lines, third and fourth lines, etc. of each file and output a new file for each result like this:

file1 output:

>ID_000_FLNNKGHD_01376-ID_000_KGHDAAD_06245 
-ATGAATACAGAGGAAAAAACACCGCTTGCATACAATAAATACAGAGGAAAAAACACCGCTTGCATACAAT

file2 output:

>ID_000_MGCDKLCO_02388-ID_000_KOAAFG_40481
ATGAAGGTGGAAAAAACACCGCTTGCATTTCCCCAGGAAGGTGGAAAAAACACCGCTTGCAAA

file3 output:

>ID_000_OMAMOGKP_02746-ID_000_GPAAAGVV_07764
--ATGTTGGTGGAAAAAACACCGCTTGCGGTA--AAATTGGTGG---------ACACCGCTTTT--

etc.

*note that the first line needs to start with ">" and is concatanated putting a "-" between each string, and the second line is just put together

outputs needs to be named file_1.fasta to file_n.fasta

Thanks!

I have multiple text files such as:

file1:

>ID_000_FLNNKGHD_01376 
-ATGAATACAGAGGAAAAAACACCGCTTGCATACAAT
>ID_000_MGCDKLCO_02388 
ATGAAGGTGGAAAAAACACCGCTTGCATTT
>ID_000_OMAMOGKP_02746
--ATGTTGGTGGAAAAAACACCGCTTGCGGTA

file2:

>ID_000_KGHDAAD_06245 
AAATACAGAGGAAAAAACACCGCTTGCATACAAT
>ID_000_KOAAFG_40481 
CCCCAGGAAGGTGGAAAAAACACCGCTTGCAAA
>ID_000_GPAAAGVV_07764
--AAATTGGTGG---------ACACCGCTTTT--

etc.

I need to concatenate the first and second lines, third and fourth lines, etc. of each file and output a new file for each result like this:

file1 output:

>ID_000_FLNNKGHD_01376-ID_000_KGHDAAD_06245 
-ATGAATACAGAGGAAAAAACACCGCTTGCATACAATAAATACAGAGGAAAAAACACCGCTTGCATACAAT

file2 output:

>ID_000_MGCDKLCO_02388-ID_000_KOAAFG_40481
ATGAAGGTGGAAAAAACACCGCTTGCATTTCCCCAGGAAGGTGGAAAAAACACCGCTTGCAAA

file3 output:

>ID_000_OMAMOGKP_02746-ID_000_GPAAAGVV_07764
--ATGTTGGTGGAAAAAACACCGCTTGCGGTA--AAATTGGTGG---------ACACCGCTTTT--

etc.

*note that the first line needs to start with ">" and is concatanated putting a "-" between each string, and the second line is just put together

outputs needs to be named file_1.fasta to file_n.fasta

Thanks!

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asked Aug 4, 2019 at 17:06

Manuel

Concatenate specific lines and output the results in a new file

I have multiple .fasta files such as:

file1:

>ID_000_FLNNKGHD_01376 
-ATGAATACAGAGGAAAAAACACCGCTTGCATACAAT
>ID_000_MGCDKLCO_02388 
ATGAAGGTGGAAAAAACACCGCTTGCATTT
>ID_000_OMAMOGKP_02746
--ATGTTGGTGGAAAAAACACCGCTTGCGGTA

file2:

>ID_000_KGHDAAD_06245 
AAATACAGAGGAAAAAACACCGCTTGCATACAAT
>ID_000_KOAAFG_40481 
CCCCAGGAAGGTGGAAAAAACACCGCTTGCAAA
>ID_000_GPAAAGVV_07764
--AAATTGGTGG---------ACACCGCTTTT--

etc.

I need to concatenate the first and second lines, third and fourth lines, etc. of each file and output a new file for each result like this:

file1 output:

>ID_000_FLNNKGHD_01376-ID_000_KGHDAAD_06245 
-ATGAATACAGAGGAAAAAACACCGCTTGCATACAATAAATACAGAGGAAAAAACACCGCTTGCATACAAT

file2 output:

>ID_000_MGCDKLCO_02388-ID_000_KOAAFG_40481
ATGAAGGTGGAAAAAACACCGCTTGCATTTCCCCAGGAAGGTGGAAAAAACACCGCTTGCAAA

file3 output:

>ID_000_OMAMOGKP_02746-ID_000_GPAAAGVV_07764
--ATGTTGGTGGAAAAAACACCGCTTGCGGTA--AAATTGGTGG---------ACACCGCTTTT--

etc.

*note that the first line needs to start with ">" and is concatanated putting a "-" between each string, and the second line is just put together

outputs needs to be named file_1.fasta to file_n.fasta

Thanks!

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