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Add option for csv input format

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This commit is contained in:
Eric Coissac
2025-03-08 07:21:24 +01:00
parent fbe7d15dc3
commit 706b44c37f
3 changed files with 15 additions and 1 deletions
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2
pkg/obioptions/version.go
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@ -8,7 +8,7 @@ import (
// corresponds to the last commit, and not the one when the file will be // corresponds to the last commit, and not the one when the file will be
// commited // commited
var _Commit = "b5cf586" var _Commit = "fbe7d15"
var _Version = "Release 4.4.0" var _Version = "Release 4.4.0"
// Version returns the version of the obitools package. // Version returns the version of the obitools package.

6
pkg/obitools/obiconvert/options.go
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@ -23,6 +23,7 @@ var __input_embl_format__ = false
var __input_genbank_format__ = false var __input_genbank_format__ = false
var __input_fastq_format__ = false var __input_fastq_format__ = false
var __input_fasta_format__ = false var __input_fasta_format__ = false
var __input_csv_format__ = false
var __output_in_fasta__ = false var __output_in_fasta__ = false
var __output_in_fastq__ = false var __output_in_fastq__ = false
@ -65,6 +66,9 @@ func InputOptionSet(options *getoptions.GetOpt) {
options.BoolVar(&__input_fasta_format__, "fasta", __input_fasta_format__, options.BoolVar(&__input_fasta_format__, "fasta", __input_fasta_format__,
options.Description("Read data following the fasta format.")) options.Description("Read data following the fasta format."))
options.BoolVar(&__input_csv_format__, "csv", __input_csv_format__,
options.Description("Read data following the CSV format."))
options.BoolVar(&__no_ordered_input__, "no-order", __no_ordered_input__, options.BoolVar(&__no_ordered_input__, "no-order", __no_ordered_input__,
options.Description("When several input files are provided, "+ options.Description("When several input files are provided, "+
"indicates that there is no order among them.")) "indicates that there is no order among them."))
@ -139,6 +143,8 @@ func CLIInputFormat() string {
return "embl" return "embl"
case __input_genbank_format__: case __input_genbank_format__:
return "genbank" return "genbank"
case __input_csv_format__:
return "csv"
default: default:
return "guessed" return "guessed"
} }

8
pkg/obitools/obiconvert/sequence_reader.go
View File

@ -126,6 +126,12 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
iterator, err = obiformats.ReadEMBL(os.Stdin, opts...) iterator, err = obiformats.ReadEMBL(os.Stdin, opts...)
case "genbank": case "genbank":
iterator, err = obiformats.ReadGenbank(os.Stdin, opts...) iterator, err = obiformats.ReadGenbank(os.Stdin, opts...)
case "fasta":
iterator, err = obiformats.ReadFasta(os.Stdin, opts...)
case "fastq":
iterator, err = obiformats.ReadFastq(os.Stdin, opts...)
case "csv":
iterator, err = obiformats.ReadCSV(os.Stdin, opts...)
default: default:
iterator = obiformats.ReadFastSeqFromStdin(opts...) iterator = obiformats.ReadFastSeqFromStdin(opts...)
} }
@ -146,6 +152,8 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
reader = obiformats.ReadFastqFromFile reader = obiformats.ReadFastqFromFile
case "fasta": case "fasta":
reader = obiformats.ReadFastaFromFile reader = obiformats.ReadFastaFromFile
case "csv":
reader = obiformats.ReadCSVFromFile
case "ecopcr": case "ecopcr":
reader = obiformats.ReadEcoPCRFromFile reader = obiformats.ReadEcoPCRFromFile
case "embl": case "embl":