weight: 150 #

Uppercase #

Convert sequences, tags, or read names to uppercase.

[[step]]
    action = "Uppercase"
    target = "read1"  # Any input segment, 'All', 'tag:mytag', or 'name:read1'
    #if_tag = "mytag"  # Optional: only apply if tag is truthy

Target Options #

Segment: "read1", "read2", "index1", "index2", or "All" - lowercase’s sequence
Tag: "tag:mytag" - lowercase’s tag’s sequence content (Location-type tags only)
Name: "name:read1" - lowercase’s read name (not including comments)

Optionally only applies if a tag is truthy via if_tag.

Examples #

Uppercase a segment #

[[step]]
    action = "Uppercase"
    target = "read1"

Uppercase a tag #

[[step]]
    action = "ExtractIUPAC"
    segment = 'read1'
    search = "CTN"
    out_label = "mytag"
    anchor = "Left"
    max_mismatches = 0

[[step]]
    action = "Uppercase"
    target = "tag:mytag"

Follow with StoreTagInSequence to apply lowercase tag back onto the read.

Uppercase read names #

[[step]]
    action = "Uppercase"
    target = "name:read1"

Conditional uppercase #

[[step]]
    action = "ExtractIUPAC"
    segment = 'read1'
    search = "CTN"
    out_label = "had_iupac"
    anchor = "Left"
    max_mismatches = 0

[[step]]
    action = "Uppercase"
    target = "read1"
    if_tag = "had_iupac"