Pages Blog. Page tree. Browse pages. A t tachments 0 Page History People who can view. Copy Page Tree. Pages Home. Sorter classes for writing, reading and sorting respectively. For compressed sequence file creations there are special classes SequenceFile. But to create an instance of any of the above writer class flavors, we use one of the static methods createWriter.
There are several overloaded versions of it but they all require at minimum, Configuration object and varargs Writer. Option… object to specify the options to create the file with. In the varargs Writer. Option , we need to specify at least file name, file system, key and value classes parameters to create the sequence file. Compression type, codec, write progress, and a Metadata instance to be stored in the SequenceFile header can be provided optionally. Once we have a SequenceFile. Writer instance, then we can write key-value pairs, using the append method.
After finishing of writing, we need to call the close method. Similar to writer instance, SequenceFile. Reader instance is used to read the sequence files and it can read any of the SequenceFile formats created with above Writer instance.
Instance of SequenceFile. The size of the 'block' is configurable. Use createWriter Configuration, Writer. CompressionType compressionType, CompressionCodec codec, org. Metadata metadata Deprecated.
CompressionType compressionType Deprecated. CompressionType compressionType, Progressable progress Deprecated. The markdown format allows the page to load with proper formatting. Now that we've covered basic text-based file formats, let's move into more bioinformatics-specific file types. FASTA pronounced "fast-A" format is a simple type of format that bioinformaticians use to represent either nucleotide or protein sequences.
It is written in text format, allowing for processing tools to easily parse the data. The general file extension is. The format allows you to precede each sequence with a comment. There are two lines per sequence - 1 the identifier comments, annotations and 2 the sequence itself.
Pretty simple, right? The top line holds information pertaining to the sequence below. Without this informative first line, we just have a raw format. Here is a list of major database sequence identifers:. The line immediately proceeding the identifier is the raw sequence. For more specific types, we can use the following:. This is a single file with several sequences, and is often used for multi-alignment programs like ClustalW or multialign. The FASTA format is extremely simple with just two lines per sequence - the first is for the description, the other for the raw sequence.
The simplicity is nice when running a quick pairwise alignment, but limiting when we need more information per sequence. With next-generation sequencing instruments pumping out millions of reads per run, scientists needed a way to check the quality of each base call. To document both the sequence and the probability of each of being correct, scientists came up with the FASTQ format. The "Q" comes from quality, as in the quality of the read. In addition to storing biological sequence information, it also adds a line for the quality scores.
The first line begins with an ' ' character and contains the sequence identifier with an optional description. The fourth line encodes the quality scores per each base call. This line must have the same length as the sequence in line 2. Scores range from! The p is the probability that the corresponding base call is incorrect, and Q is the Phred quality score which can range from 0 to SAMtools is a suite of utilities that allow for efficient post-processing of short DNA sequence read alignments.
The program includes several command line programs such as view , sort , and index that allow for next-generation sequence data processing. In addition to regular sequence reads, SAM includes alignment data that link short reads to a reference sequence.
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