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.