ConvertHeaders¶

Converts sequence headers to the pRESTO format

usage: ConvertHeaders [--version] [-h]  ...

--version¶: show program’s version number and exit

-h, --help¶: show this help message 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 454 [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                          [-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
                          [--outname OUT_NAME] [--failed] [--fasta]
                          [--delim DELIMITER DELIMITER DELIMITER]

--version¶: show program’s version number and exit

-h, --help¶: show this help message and exit

-s <seq_files>¶: A list of FASTA/FASTQ files containing sequences to process.

-o <out_files>¶: Explicit output file name(s). Note, this argument cannot be used with the –failed, –outdir, or –outname arguments. If unspecified, then the output filename will be based on the input filename(s).

--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.

--failed¶: If specified create files containing records that fail processing.

--fasta¶: Specify to force output as FASTA rather than FASTQ.

--delim <delimiter>¶: A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

ConvertHeaders genbank¶

Converts NCBI GenBank and RefSeq: sequence headers.

usage: ConvertHeaders genbank [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                              [-o OUT_FILES [OUT_FILES ...]]
                              [--outdir OUT_DIR] [--outname OUT_NAME]
                              [--failed] [--fasta]
                              [--delim DELIMITER DELIMITER DELIMITER]

--version¶: show program’s version number and exit

-h, --help¶: show this help message and exit

-s <seq_files>¶: A list of FASTA/FASTQ files containing sequences to process.

-o <out_files>¶: Explicit output file name(s). Note, this argument cannot be used with the –failed, –outdir, or –outname arguments. If unspecified, then the output filename will be based on the input filename(s).

--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.

--failed¶: If specified create files containing records that fail processing.

--fasta¶: Specify to force output as FASTA rather than FASTQ.

--delim <delimiter>¶: A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

ConvertHeaders generic¶

Converts sequence headers without a known: annotation system.

usage: ConvertHeaders generic [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                              [-o OUT_FILES [OUT_FILES ...]]
                              [--outdir OUT_DIR] [--outname OUT_NAME]
                              [--failed] [--fasta]
                              [--delim DELIMITER DELIMITER DELIMITER]

--version¶: show program’s version number and exit

-h, --help¶: show this help message and exit

-s <seq_files>¶: A list of FASTA/FASTQ files containing sequences to process.

-o <out_files>¶: Explicit output file name(s). Note, this argument cannot be used with the –failed, –outdir, or –outname arguments. If unspecified, then the output filename will be based on the input filename(s).

--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.

--failed¶: If specified create files containing records that fail processing.

--fasta¶: Specify to force output as FASTA rather than FASTQ.

--delim <delimiter>¶: A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

ConvertHeaders illumina¶

Converts Illumina sequence headers.

usage: ConvertHeaders illumina [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                               [-o OUT_FILES [OUT_FILES ...]]
                               [--outdir OUT_DIR] [--outname OUT_NAME]
                               [--failed] [--fasta]
                               [--delim DELIMITER DELIMITER DELIMITER]

--version¶: show program’s version number and exit

-h, --help¶: show this help message and exit

-s <seq_files>¶: A list of FASTA/FASTQ files containing sequences to process.

-o <out_files>¶: Explicit output file name(s). Note, this argument cannot be used with the –failed, –outdir, or –outname arguments. If unspecified, then the output filename will be based on the input filename(s).

--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.

--failed¶: If specified create files containing records that fail processing.

--fasta¶: Specify to force output as FASTA rather than FASTQ.

--delim <delimiter>¶: A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

ConvertHeaders imgt¶

Converts sequence headers output by: IMGT/GENE-DB.

usage: ConvertHeaders imgt [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                           [-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
                           [--outname OUT_NAME] [--failed] [--fasta]
                           [--delim DELIMITER DELIMITER DELIMITER] [--simple]

--version¶: show program’s version number and exit

-h, --help¶: show this help message and exit

-s <seq_files>¶: A list of FASTA/FASTQ files containing sequences to process.

-o <out_files>¶: Explicit output file name(s). Note, this argument cannot be used with the –failed, –outdir, or –outname arguments. If unspecified, then the output filename will be based on the input filename(s).

--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.

--failed¶: If specified create files containing records that fail processing.

--fasta¶: Specify to force output as FASTA rather than FASTQ.

--delim <delimiter>¶: A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

--simple¶: If specified, only the allele name, and no other annotations, will appear in the converted sequence header.

ConvertHeaders migec¶

Converts headers for consensus sequence generated: by the MIGEC tool.

usage: ConvertHeaders migec [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                            [-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
                            [--outname OUT_NAME] [--failed] [--fasta]
                            [--delim DELIMITER DELIMITER DELIMITER]

--version¶: show program’s version number and exit

-h, --help¶: show this help message and exit

-s <seq_files>¶: A list of FASTA/FASTQ files containing sequences to process.

-o <out_files>¶: Explicit output file name(s). Note, this argument cannot be used with the –failed, –outdir, or –outname arguments. If unspecified, then the output filename will be based on the input filename(s).

--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.

--failed¶: If specified create files containing records that fail processing.

--fasta¶: Specify to force output as FASTA rather than FASTQ.

--delim <delimiter>¶: A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

ConvertHeaders sra¶

Converts NCBI SRA or EMBL-EBI ENA sequence headers.

usage: ConvertHeaders sra [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                          [-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
                          [--outname OUT_NAME] [--failed] [--fasta]
                          [--delim DELIMITER DELIMITER DELIMITER]

--version¶: show program’s version number and exit

-h, --help¶: show this help message and exit

-s <seq_files>¶: A list of FASTA/FASTQ files containing sequences to process.

-o <out_files>¶: Explicit output file name(s). Note, this argument cannot be used with the –failed, –outdir, or –outname arguments. If unspecified, then the output filename will be based on the input filename(s).

--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.

--failed¶: If specified create files containing records that fail processing.

--fasta¶: Specify to force output as FASTA rather than FASTQ.

--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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