csv2fasta

Description

Convert two columns from a CSV file to FASTA entries. The CSV file can
contain an optional header and each row (other than the header) becomes
a single FASTA record. One of the two columns will be used as the names
for the FASTA entries, while the other become the sequences. The sequences
column must only contain characters that are valid IUPAC notation for
nucleotides or a group thereof (wildcard characters).

Type

python_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.fasta"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/craftbox.git \  
  -revision v0.3.3 \  
  -main-script target/nextflow/csv2fasta/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	CSV file to be processed.
--header	boolean_true	Parse the first line of the CSV file as a header.

Name

Type & Properties

--input

file

required

--header

boolean_true

CSV dialect options

Name	Type & Properties	Description
--delimiter	string	Overwrite the column delimiter character.
--quote_character	string	Overwrite the character used to denote the start and end of a quoted item.

Name

Type & Properties

--delimiter

string

--quote_character

string

CSV column arguments

Name	Type & Properties	Description
--sequence_column	string	Name of the column containing the sequences. Implies 'header'. Cannot be used together with 'sequence_column_index'.
--name_column	string	Name of the column describing the FASTA headers. Implies 'header'. Cannot be used together with 'name_column_index'.
--sequence_column_index	integer	Index of the column to use as the FASTA sequences, counter from the left and starting from 0. Cannot be used in combination with the 'sequence_column' argument.
--name_column_index	integer	Index of the column to use as the FASTA headers, counter from the left and starting from 0. Cannot be used in combination with 'name_column'.

Name

Type & Properties

--sequence_column

string

--name_column

string

--sequence_column_index

integer

--name_column_index

integer

Outputs

Name	Type & Properties	Description
--output	file output	Output fasta file.

Name

Type & Properties

--output

file

output