topic Extract portion of taxonomic string (i.e., kingdom, phyla, etc.) in SAS Programming

Extract portion of taxonomic string (i.e., kingdom, phyla, etc.)

lsandell — Thu, 04 May 2023 22:35:46 GMT

Hi there! I have taxonomic data with the phyla through genus listed from microbiome 16s sequencing. I want to pull just the 'Family' name out of the string, but each character string is different due to the nature of each taxonomy identified within the sample.

I have included a screenshot of the character variable "taxon" that has this string information. It's a character variable with 106 length. (I cannot share the data in full so I hope the image is enough context). Is there an approach you'd recommend taking to pull out this substring from variable starting positions? I do have a delimiter of sorts - the " / ". The most efficient method would be useful as I have over 1 million records.

Thank you!

Re: Extract portion of taxonomic string (i.e., kingdom, phyla, etc.)

sbxkoenk — Thu, 04 May 2023 22:46:49 GMT

@lsandell wrote:

I want to pull just the 'Family' name out of the string, ...

What is the 'Family' name in the strings listed?

What is the substring you need as an outcome after parsing every taxon string?

Koen

Re: Extract portion of taxonomic string (i.e., kingdom, phyla, etc.)

SASKiwi — Thu, 04 May 2023 22:50:21 GMT

So what is your business rule for identifying the family name in the string?

Re: Extract portion of taxonomic string (i.e., kingdom, phyla, etc.)

lsandell — Fri, 05 May 2023 01:02:22 GMT

Thanks! It's the name before the final forward slash (/) [i.e., second to last alphabetic portion].

Re: Extract portion of taxonomic string (i.e., kingdom, phyla, etc.)

lsandell — Fri, 05 May 2023 01:03:34 GMT

Just one word from the whole string (what's in between the slashes). The target string is the name before the final forward slash (/) [i.e., second to last alphabetic portion].

Re: Extract portion of taxonomic string (i.e., kingdom, phyla, etc.)

SASKiwi — Fri, 05 May 2023 01:29:06 GMT

Try this. The SCAN function is finding the second word reading from the right:

data test;
  string = 'w1/w2/w3/w4/w5/w6';
  Family = scan(string,-2,'/');
  put _all_;
run;