topic Re: Creating a FASTA file from dataset in ODS and Base Reporting

Creating a FASTA file from dataset

HabAM — Fri, 21 Jun 2019 17:35:49 GMT

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.

Re: Creating a FASTA file from dataset

Reeza — Fri, 21 Jun 2019 17:37:35 GMT

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.

Re: Creating a FASTA file from dataset

HabAM — Fri, 21 Jun 2019 18:18:27 GMT

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

Re: Creating a FASTA file from dataset

Kurt_Bremser — Fri, 21 Jun 2019 18:23:26 GMT

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

Re: Creating a FASTA file from dataset

Reeza — Fri, 21 Jun 2019 18:29:45 GMT

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;

@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