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.