Creating a FASTA file from dataset

[HabAM]

Hello,

I am trying to convert a SAS dataset with nucleotide sequence to a fasta format. See sample FASTA formated file here:https://github.com/veg/hivtrace/blob/master/test/rsrc/TEST.FASTA

What I have is a table with two columns:

ID Seq

What I need is to create a new line for the corresponding Seq value as :

>ID1
Seq1

>ID2

Seq2

Any advise is much appreciated.

[Reeza]

Just use a PUT statement.

data _null_;
file 'myfile.txt';

put ID;
put Seq1;

run;

You may want to control line length so it defaults and flows over but otherwise that should really be all you need to get started.

[HabAM]

Thank you Reeza. The only issue is I have thousands of row values to individually list as suggested. 

samle set 

ID	Seq
>12121	aaatatgttgactcagattggttgtactttaaattttccaattagtcctattgaaactgtaccagtaaaattgaagccag
>343434	cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg
>4545e	cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg
>1111	cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg
>2321	cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg

expected text file:

>12121

aaatatgttgactcagattggttgtactttaaattttccaattagtcctattgaaactgtaccagtaaaattgaagccag

>343434

cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg

>4545e

cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg

>1111

cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg

>2321

cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg

Thank you

[Kurt_Bremser]

Add the necessary set statement to @Reeza 's code in order to read your SAS dataset.

[Reeza · Accepted solution]

You don't list the individual values, you list the variable names.

Run this, changing the filepath to be relevant as a starting point and see what is generated.

data _null_;

set sashelp.class;

file '/folders/myfolders/demo.txt' linesize=80 flowover;

put Name;
put Age;

run;

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@HabAM wrote:

Thank you Reeza. The only issue is I have thousands of row values to individually list as suggested. 

samle set 

ID	Seq
>12121	aaatatgttgactcagattggttgtactttaaattttccaattagtcctattgaaactgtaccagtaaaattgaagccag
>343434	cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg
>4545e	cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg
>1111	cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg
>2321	cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg

expected text file:

>12121

aaatatgttgactcagattggttgtactttaaattttccaattagtcctattgaaactgtaccagtaaaattgaagccag

>343434

cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg

>4545e

cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg

>1111

cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg

>2321

cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg

Thank you

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