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.

Additional, there’s a series of virtual tags available:

len_<segment-name> - the length of the specified segment (e.g. len_read1).
len_<tag-label> - the length of the specified tag (e.g. len_mytag). For location tags, this is the length of the underlying matched regions (which may change / be lost when reads are truncated - eval before truncation if necessary). For string tags (= ExtractRegex with source=name:...) this is the length of the replaced string.
read_no - the running number of the read (starting with 0)

Language #

Besides the regular arithmetic operators (+, -, *, /, %, ^) this supports log(base, val), e(), pi(), int(), ceil(), floor(), round(), abs(), sign(), min(a,b,…), max(a,b,…) sin(radians), cos(radians), tan(radians), sinh(radians), cosh(radians), tanh(radians), Use any defined tag by name. Location/string tags are converted to booleans by their presence.

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).