From fd4c7c2572953e37b641c680d32ee93d7d1b87cd Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Mon, 14 Aug 2023 00:12:17 +0200 Subject: [PATCH] Adds some docs Former-commit-id: 7e96983ed707b2a574425799c32c32243f4876cf --- pkg/obiformats/fastseq_write_fasta.go | 7 +++++++ pkg/obiformats/fastseq_write_fastq.go | 2 ++ 2 files changed, 9 insertions(+) diff --git a/pkg/obiformats/fastseq_write_fasta.go b/pkg/obiformats/fastseq_write_fasta.go index 0d050cf..9fdb9e4 100644 --- a/pkg/obiformats/fastseq_write_fasta.go +++ b/pkg/obiformats/fastseq_write_fasta.go @@ -1,3 +1,4 @@ +// Package obiformats provides functions for formatting and writing biosequences in various formats. package obiformats import ( @@ -23,6 +24,7 @@ func min(x, y int) int { return y } +// FormatFasta formats a BioSequence as a FASTA-formatted string using the provided format header. func FormatFasta(seq *obiseq.BioSequence, formater FormatHeader) string { var fragments strings.Builder @@ -55,6 +57,7 @@ func FormatFasta(seq *obiseq.BioSequence, formater FormatHeader) string { folded) } +// FormatFastaBatch formats a batch of BioSequences as a single FASTA-formatted byte slice using the provided format header. func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader, skipEmpty bool) []byte { var bs bytes.Buffer for _, seq := range batch.Slice() { @@ -72,6 +75,7 @@ func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader, ski return bs.Bytes() } +// The WriteFasta function writes a given iterator of biological sequences to a file in FASTA format. func WriteFasta(iterator obiiter.IBioSequence, file io.WriteCloser, options ...WithOption) (obiiter.IBioSequence, error) { @@ -154,12 +158,15 @@ func WriteFasta(iterator obiiter.IBioSequence, return newIter, nil } +// The function WriteFastaToStdout writes a FASTA file to standard output. func WriteFastaToStdout(iterator obiiter.IBioSequence, options ...WithOption) (obiiter.IBioSequence, error) { options = append(options, OptionDontCloseFile()) return WriteFasta(iterator, os.Stdout, options...) } +// The function `WriteFastaToFile` writes a given iterator of biosequences to a file in FASTA format, +// with the option to append to an existing file and save paired sequences to a separate file. func WriteFastaToFile(iterator obiiter.IBioSequence, filename string, options ...WithOption) (obiiter.IBioSequence, error) { diff --git a/pkg/obiformats/fastseq_write_fastq.go b/pkg/obiformats/fastseq_write_fastq.go index 1d2c695..d3c6774 100644 --- a/pkg/obiformats/fastseq_write_fastq.go +++ b/pkg/obiformats/fastseq_write_fastq.go @@ -15,6 +15,8 @@ import ( "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils" ) +// The function FormatFastq takes a BioSequence object, a quality shift value, and a header formatter +// function as input, and returns a formatted string in FASTQ format. func FormatFastq(seq *obiseq.BioSequence, quality_shift int, formater FormatHeader) string { l := seq.Len()