ConvertHeaders.py
Converts sequence headers to the pRESTO format
usage: ConvertHeaders.py [--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.py 454
Converts Roche 454 sequence headers.
usage: ConvertHeaders.py 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.py genbank
Converts NCBI GenBank and RefSeq sequence headers.
usage: ConvertHeaders.py 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.py generic
Converts sequence headers without a known annotation system.
usage: ConvertHeaders.py 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.py illumina
Converts Illumina sequence headers.
usage: ConvertHeaders.py 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.py imgt
Converts sequence headers output by IMGT/GENE-DB.
usage: ConvertHeaders.py 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.py migec
Converts headers for consensus sequence generated by the MIGEC tool.
usage: ConvertHeaders.py 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.py sra
Converts NCBI SRA or EMBL-EBI ENA sequence headers.
usage: ConvertHeaders.py 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.