Tag Conversion on fastqrab documentation

Mon, 01 Jan 0001 00:00:00 +0000

ConvertRegionsToLength #

Turn region tags (such as those produced by ExtractRegion/ExtractRegions) into numeric length tags.

[[step]]
 action = "ExtractRegion"
 out_label = "adapter"
 source = "read1"
 start = 0
 len = 12
 anchor = "Start"

[[step]]
 action = "ConvertRegionsToLength"
 out_label = "adapter_len"
 in_label = "adapter"

The new tag stores the total span (in bases) covered by all regions on each read.
Reads without the source tag receive a length of 0.
label must be different from region_label; the step keeps the original region tag.

Mon, 01 Jan 0001 00:00:00 +0000

EvalExpression #

[[step]]
 action = "EvalExpression"
 out_label = "outtag"
 expression = "log(2, mytag + 1)" # log to base 2
 result_type = "numeric" # or bool.

Calculate a fasteval expression on your tags, which you can then pass to .FilterByTag.

You can use any tags previously defined on the molecule as variables in the expression.

Location/String tags get converted into bools (false=0, true=1) based on whether they are present (=not missing).

That means you can for example chain this after HammingCorrect with on_no_match = ‘remove’.

Compare String Tags

Mon, 01 Jan 0001 00:00:00 +0000

CompareStringTags #

[[step]]
 action = "CompareStringTags"
 in_label_a = "tag_a" # First string or location tag to compare
 in_label_b = "tag_b" # Second string or location tag to compare
 out_label = "cmp" # Numeric output: -1, 0, or 1 for smaller, equal, larger

Compare two string- or location-valued tags lexicographically (byte-by-byte).

The output tag is numeric:

-1 if tag_a < tag_b
0 if tag_a == tag_b
1 if tag_a > tag_b

Both tags must contain sequences of the same length for every read. A runtime error is raised for any read where the two sequences have different lengths.

Convert To Rate

Mon, 01 Jan 0001 00:00:00 +0000

ConvertToRate #

[[step]]
 action = "CalcBaseContent"
 segment = "read1"
 bases_to_count = "A"
 relative = false
 out_label = "a_count" # absolute A-base count

[[step]]
 action = "ConvertToRate"
 in_label = "a_count" # The numeric tag to divide by read length
 out_label = "a_rate" # Output tag label
 segment = "read1" # Segment to measure length from, or 'All' for total length (default: only segment if single-read input)

Divide an existing numeric tag by the read length to produce a normalized rate.

Typical use case: Divide EvalExpression by the read length to get a fraction (rate).