export_trace
Read-only
Write a Sanger read out in any of the eight formats the trace editor's Export section offers, and hand the file back as TEXT in the pipeline rather than as a download. Reports what the chosen target DROPPED — a read written as FASTA loses its annotations, and every target but FASTQ loses the per-base quality — because those losses are invisible in the file itself. Trims the ends first when asked, by the same three methods the Trim section offers, so a graph does not need a separate step to write a trimmed read.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| trim | No | trim the ends before writing, the same three ways the Trim section does. `none` writes the file's calls as they are; `auto` uses the file's own Mott record when it has one and the sliding window when it does not; `mott` is the instrument's record, which SCF and ZTR never carry; `window` always computes it here. | none |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| format | No | the target. FASTQ is the only one that carries the per-base Phred; GenBank and EMBL are the only two that carry annotations; the rest are a bare sequence. | fasta |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| document | No | which trace file to write: its name (`read_F.ab1`) or its project file id. A file id is project-specific, so a template ships this unset. | |
| use_internal_name | No | name the record and the filename from the instrument's own sample record (ABIF `SMPL`) rather than from the file name. The instrument's name is often a plate well that means nothing outside the run; a file with no internal record uses its filename either way, and says so. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| text | Yes | the file, as text. A VALUE and not a download, deliberately: a graph step that wrote to disk could not be composed with the step after it | |
| bases | Yes | how many bases the file carries | |
| reading | Yes | the same sentence the editor shows for this export, generated from it | |
| filename | Yes | the name this would be saved as, with the user's own extension for this format applied | |
| sequence | Yes | just the bases that were written, so a downstream step does not have to parse the record back apart | |
| trimUsed | Yes | which trim actually ran. `auto` answers `window` on a file with no Mott record, so a pipeline that assumed otherwise trimmed on a threshold nobody chose — the same trap `trim_trace`'s `methodUsed` exists for | |
| fileBases | Yes | how many calls the trace file holds. Read it against `bases`: the difference is what the bounds cut | |
| lastBaseKept | Yes | 1-based inclusive | |
| firstBaseKept | Yes | 1-based inclusive, the same convention `trim_trace` reports in and every trim readout in the editor uses | |
| carriedQuality | Yes | whether the per-base Phred reached the file. False on every target but FASTQ, and on a read that never had one |