ConvertHeaders¶
Converts sequence headers to the pRESTO format
usage: ConvertHeaders [-h] [–version] ...
-
-h,--help¶ show this help message and exit
-
--version¶ show program’s version number and exit
- output files:
- convert-pass
- reads passing header conversion.
- convert-fail
- raw reads failing header conversion.
- output annotation fields:
- <format defined>
- the annotation fields added are specific to the header format of the input file.
ConvertHeaders 454¶
Converts Roche 454 sequence headers.
usage: ConvertHeaders [-h] [–version] ...
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-h,--help¶ show this help message and exit
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-s<seq_files>¶ A list of FASTA/FASTQ files containing sequences to process.
-
--fasta¶ Specify to force output as FASTA rather than FASTQ.
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--failed¶ If specified create files containing records that fail processing.
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--delim<delimiter>¶ A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.
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--outdir<out_dir>¶ Specify to changes the output directory to the location specified. The input file directory is used if this is not specified.
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--outname<out_name>¶ Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files.
ConvertHeaders genbank¶
Converts NCBI GenBank and RefSeq sequence headers.
usage: ConvertHeaders [-h] [–version] ...
-
-h,--help¶ show this help message and exit
-
-s<seq_files>¶ A list of FASTA/FASTQ files containing sequences to process.
-
--fasta¶ Specify to force output as FASTA rather than FASTQ.
-
--failed¶ If specified create files containing records that fail processing.
-
--delim<delimiter>¶ A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.
-
--outdir<out_dir>¶ Specify to changes the output directory to the location specified. The input file directory is used if this is not specified.
-
--outname<out_name>¶ Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files.
ConvertHeaders generic¶
Converts sequence headers without a known annotation system.
usage: ConvertHeaders [-h] [–version] ...
-
-h,--help¶ show this help message and exit
-
-s<seq_files>¶ A list of FASTA/FASTQ files containing sequences to process.
-
--fasta¶ Specify to force output as FASTA rather than FASTQ.
-
--failed¶ If specified create files containing records that fail processing.
-
--delim<delimiter>¶ A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.
-
--outdir<out_dir>¶ Specify to changes the output directory to the location specified. The input file directory is used if this is not specified.
-
--outname<out_name>¶ Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files.
ConvertHeaders illumina¶
Converts Illumina sequence headers.
usage: ConvertHeaders [-h] [–version] ...
-
-h,--help¶ show this help message and exit
-
-s<seq_files>¶ A list of FASTA/FASTQ files containing sequences to process.
-
--fasta¶ Specify to force output as FASTA rather than FASTQ.
-
--failed¶ If specified create files containing records that fail processing.
-
--delim<delimiter>¶ A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.
-
--outdir<out_dir>¶ Specify to changes the output directory to the location specified. The input file directory is used if this is not specified.
-
--outname<out_name>¶ Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files.
ConvertHeaders imgt¶
Converts sequence headers output by IMGT/GENE-DB.
usage: ConvertHeaders [-h] [–version] ...
-
-h,--help¶ show this help message and exit
-
-s<seq_files>¶ A list of FASTA/FASTQ files containing sequences to process.
-
--fasta¶ Specify to force output as FASTA rather than FASTQ.
-
--failed¶ If specified create files containing records that fail processing.
-
--delim<delimiter>¶ A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.
-
--outdir<out_dir>¶ Specify to changes the output directory to the location specified. The input file directory is used if this is not specified.
-
--outname<out_name>¶ Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files.
-
--simple¶ If specified, only the allele name, and no other annotations, will appear in the converted sequence header.
ConvertHeaders sra¶
Converts NCBI SRA sequence headers.
usage: ConvertHeaders [-h] [–version] ...
-
-h,--help¶ show this help message and exit
-
-s<seq_files>¶ A list of FASTA/FASTQ files containing sequences to process.
-
--fasta¶ Specify to force output as FASTA rather than FASTQ.
-
--failed¶ If specified create files containing records that fail processing.
-
--delim<delimiter>¶ A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.
-
--outdir<out_dir>¶ Specify to changes the output directory to the location specified. The input file directory is used if this is not specified.
-
--outname<out_name>¶ Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files.