Write a read as an ABIF (.ab1) trace file

Writes a minimal ABIF file with the four trace channels (DATA9–DATA12, in the order given by FWO_1), the sample name (SMPL1), and the base calls, quality scores and peak positions.

Usage

write_abif(read, file, basecaller = FALSE)

Arguments

read

A list with elements name, bases, quality, peaks and traces, as returned by read_spf().

file

Path of the file to write.

basecaller

If TRUE, also write the base calls, quality scores and peak positions to the base-caller tags PBAS2, PCON2 and PLOC2.

Value

file, invisibly.

Details

ABIF keeps two sets of base calls: PBAS1, PCON1 and PLOC1 hold the calls, quality scores and peak positions as edited by the user, and PBAS2, PCON2 and PLOC2 hold them as called by the base caller. A Sequencher project keeps only the edited set, and it does not record which reads were edited, so by default write_abif() fills only the edited tags.

Some readers need the base-caller tags. Biopython's SeqIO.read() raises an error on a file without PBAS2, and sangerseqR::readsangerseq() fails without PBAS2 and PLOC2. Set basecaller = TRUE to copy the values into those tags as well, so that these tools can read the file. The copies are then labelled as base-caller output even where the read was edited in Sequencher.