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 ...]
                              [--fasta] [--failed]
                              [--delim DELIMITER DELIMITER DELIMITER]
                              [--outdir OUT_DIR] [--outname OUT_NAME]
--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.

--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 genbank

Converts NCBI GenBank and RefSeq
sequence headers.
usage: ConvertHeaders genbank [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                                  [--fasta] [--failed]
                                  [--delim DELIMITER DELIMITER DELIMITER]
                                  [--outdir OUT_DIR] [--outname OUT_NAME]
--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.

--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 generic [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                                  [--fasta] [--failed]
                                  [--delim DELIMITER DELIMITER DELIMITER]
                                  [--outdir OUT_DIR] [--outname OUT_NAME]
--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.

--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 illumina [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                                   [--fasta] [--failed]
                                   [--delim DELIMITER DELIMITER DELIMITER]
                                   [--outdir OUT_DIR] [--outname OUT_NAME]
--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.

--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 imgt [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                               [--fasta] [--failed]
                               [--delim DELIMITER DELIMITER DELIMITER]
                               [--outdir OUT_DIR] [--outname OUT_NAME] [--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.

--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 sra [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                              [--fasta] [--failed]
                              [--delim DELIMITER DELIMITER DELIMITER]
                              [--outdir OUT_DIR] [--outname OUT_NAME]
--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.

--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.