lists

Including metadata (lists)

It often occurs that information from text files (created manually or using another program) needs to be associated with sequences. Such metadata can be included using the -l / --list option. Sequence IDs are expected to be in the first column. If not, specify --id-col.

Fields are accessible as variables in this form: l:<column_index> or l:<column_name>. Consider this list containing taxonomic information about sequences (taxonomy.txt):

id  lineage
seq1  d:Bacteria,p:"Actinobacteria",c:Actinobacteria,o:Actinomycetales,f:Actinomycetaceae,g:Actinomyces;
seq2  d:Bacteria,p:"Actinobacteria",c:Actinobacteria,o:Actinomycetales,f:Pseudonocardiaceae,g:Amycolatopsis;
(...)

The lineages can be added to the FASTA header using this command:

st set -l taxonomy.txt -d {l:lineage} seqs.fa > seqs_with_taxonomy.fa

seqs_with_taxonomy.fa:

>seq1 d:Bacteria,p:"Actinobacteria",c:Actinobacteria,o:Actinomycetales,f:Actinomycetaceae,g:Actinomyces;
SEQUENCE
>seq2 d:Bacteria,p:"Actinobacteria",c:Actinobacteria,o:Actinomycetales,f:Pseudonocardiaceae,g:Amycolatopsis;
SEQUENCE
(...)

By default IDs in the text file (first column) are expected to be in the same order as sequence IDs. If not, there will be an error message:

ID mismatch: expected 'seq1' but found 'seq12'. Use -u/--unordered if sequences and lists are not in same order.

Therefore we add -u. This will consume more memory, especially if the list file is large.

st set -ul taxonomy.txt -d {l:lineage} seqs.fa > seqs_with_taxonomy.fa

Additionally, the tool expects all IDs to be present in associated list. If this is not true, it is necessary to explicitly to specify -m/--missing.

Filtering given an ID list

It is possible to keep/exclude sequences based on whether they occur in a list or not. This can be achieved by using the filter command. The def() function returns true if the ID (in the first column here) is present.

st filter -uml id_list.txt "def(l:1)" seqs.fa > in_list.fa