BlastTabularLL - SeqAn API Documentation

# Class BlastTabularLL
Low-Level support for Blast Tabular file formats

Defined in | <seqan/blast.h>
Signature | `typedef Tag<BlastTabularLL_> BlastTabularLL;`

## Interface Function Overview

- `bool onMatch(stream, blastTabularLL)`
  Returns whether the iterator is on the beginning of a match line.
- `void readMatch(stream, blastTabularLL, args ...);`
  Low-level BlastTabular file reading.
- `void skipUntilMatch(stream, blastTabularLL);`
  Skip arbitrary number of comment lines until the beginning of a match is reached.
- `void writeMatch(stream, blastTabularLL, columns...)`
  Low-level file-writing for blast tabular formats

## Detailed Description

There are three blast format related tags in SeqAn:

- BlastReport with the FormattedFile output specialization BlastReportFileOut
- BlastTabular with the FormattedFile output and input specializations BlastTabularFileOut and BlastTabularFileIn
- BlastTabularLL which provides light-weight, but very basic tabular IO

This is the third tag, it offers low-level support for reading and writing NCBI Blast compatible tabular files, without comment lines -- although files with comment lines can be read if the comment lines are skipped. These are the formats that are available in legacy Blast (`blastall` executable) with the parameters `-m 8` and `-m 9` (with comment lines) and in BLAST+ (`blastx`, `blastn`...) with the parameters `-outfmt 6` and `-outfmt 7` respectively.

For most situations BlastTabular is more adequate. Use this tag's interface only for quick parsing of matches in a file, e.g counting and filtering purposes. This interface does not offer a FormattedFile abstraction and no convenience data structures, it does no transformations on the data.

The reference Blast implementation used for developing the SeqAn support is NCBI Blast+ 2.2.26 and NCBI Blast 2.2.26 for the legacy support.

### Input example

The following example program extracts the list of matching query-subject-pairs from a blast tabular file and prints it to std::out:

    #include <iostream>
    #include <seqan/basic.h>
    #ifndef STDLIB_VS
    #include <seqan/blast.h>

    using namespace seqan2;

    int main()
    {
        std::string inPath = getAbsolutePath("/tests/blast/plus_comments_defaults.m9");

        std::ifstream fin(toCString(inPath), std::ios_base::in | std::ios_base::binary);
        auto fit = directionIterator(fin, Input());

        typedef std::pair<std::string, std::string> THsp;
        std::vector<THsp> hsps;

        while (!atEnd(fit))
        {
            // skip any comment lines
            if (!onMatch(fit, BlastTabularLL()))
            {
                skipUntilMatch(fit, BlastTabularLL());
                if (atEnd(fit))
                    break;
            }

            // resize output list
            resize(hsps, length(hsps)+1);

            // read only the first two fields into our variables
            readMatch(fit, BlastTabularLL(), back(hsps).first, back(hsps).second);
        }

        std::sort(std::begin(hsps), std::end(hsps));
        auto last = std::unique(std::begin(hsps), std::end(hsps));
        hsps.erase(last, hsps.end());

        for (THsp const & hsp : hsps)
            std::cout << '(' << hsp.first << ", " << hsp.second << ")\n";

        return 0;
    }
    #else
    int main()
    {
        std::cerr << "Demo not run, because of a bug in Microsoft Visual Studio 2015.\n";
        return 0;
    }
    #endif

Demo: demos/blast/blast_in_lowlevel.cpp

The output looks like this:

    (SHAA004TF, sp|P03831|INBD_SHIDY)
    (SHAA004TF, sp|P0A915|OMPW_ECOLI)
    (SHAA004TF, sp|P0A916|OMPW_SHIFL)
    (SHAA004TF, sp|P0CF25|INSB1_ECOLI)
    (SHAA004TF, sp|P0CF26|INSB2_ECOLI)
    (SHAA004TF, sp|P0CF27|INSB3_ECOLI)
    (SHAA004TF, sp|P0CF28|INSB5_ECOLI)
    (SHAA004TF, sp|P0CF29|INSB6_ECOLI)
    (SHAA004TF, sp|P0CF30|INSB8_ECOLI)
    (SHAA004TF, sp|P0CF31|INSB_ECOLX)
    (SHAA004TF, sp|P17266|OMPW_VIBCH)
    (SHAA004TF, sp|P19765|INSB_SHIFL)
    (SHAA004TF, sp|P19766|INSB_SHISO)
    (SHAA004TF, sp|P57998|INSB4_ECOLI)
    (SHAA004TF, sp|P59843|INSB_HAEDU)
    (SHAA004TF, sp|Q8Z7E2|OMPW_SALTI)
    (SHAA004TF, sp|Q8ZP50|OMPW_SALTY)
    (SHAA004TR, sp|Q0HGZ8|META_SHESM)
    (SHAA004TR, sp|Q0HTA5|META_SHESR)

## Interface Functions Detail

### `bool onMatch(stream, blastTabularLL)`

Returns whether the iterator is on the beginning of a match line.

#### Parameters

`iter` | An input iterator over a stream or any fwd-iterator over a string.
`blastTabularLL` | The BlastTabularLL tag.

#### Returns

`bool` | true or false

#### Thrown Exceptions

`IOError` | On low-level I/O errors.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `void readMatch(stream, blastTabularLL, args ...);`

Low-level BlastTabular file reading.

#### Parameters

`stream` | An input iterator over a stream or any fwd-iterator over a string.
`blastTabularLL` | The BlastTabularLL tag.
`args` | Arbitrary typed variables able to hold the fields.

#### Remarks

Use this signature only if you do not or cannot use BlastMatches. You can specify any number of arguments that are expected to be able to hold the values in the columns read, i.e. if you pass a double as argument and the value in the column cannot be successfully cast to double, an exception will be thrown. If you want to be on the safe side, you can pass CharStrings and evaluate them in another way.

You may specify less columns than are available in the file, all but the first n will be discarded.

No transformations are made on the data, e.g. the positions are still one-indexed and flipped for reverse strand matches.

See BlastTabularLL for an example of low-level IO.

#### Thrown Exceptions

`IOError` | On low-level I/O errors.
`ParseError` | On high-level file format errors.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `void skipUntilMatch(stream, blastTabularLL);`

Skip arbitrary number of comment lines until the beginning of a match is reached.

#### Parameters

`stream` | An input iterator over a stream or any fwd-iterator over a string.
`blastTabularLL` | The BlastTabularLL tag.

#### Remarks

This is also part of the low-level IO and not required if you use readRecord. Call this function whenever you are not onMatch, but want to be, e.g. to readMatch.

Since it is legal for files to end with comment lines, this function does not throw if end-of-file is reached. You need to check that after calling.

#### Thrown Exceptions

`IOError` | On low-level I/O errors.
`ParseError` | On high-level file format errors.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

### `void writeMatch(stream, blastTabularLL, columns...)`

Low-level file-writing for blast tabular formats

#### Parameters

`stream` | The file to write to (FILE, fstream, OutputStreamConcept ...).
`blastTabularLL` | The BlastTabularLL tag.
`columns` | ... Any number of printable parameters.

#### Remarks

This is a very leight-weight alternative to writeRecord. It doesn't require BlastMatches, BlastRecords or the use of FormattedFile. It supports an arbitrary amount of and arbitrary typed columns to be printed.

Use this only if you do not require comment lines and you are prepared to do all transformations on the data yourself, i.e. this function does none of the match adjustments mentioned in writeRecord.

#### Thrown Exceptions

`IOError` | On low-level I/O errors.

#### Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

#### Dox Sources

    /*!
     * @class BlastTabularLL
     *
     * @headerfile <seqan/blast.h>
     *
     * @brief Low-Level support for Blast Tabular file formats
     *
     * @signature typedef Tag<BlastTabularLL_> BlastTabularLL;
     *
     * There are three blast format related tags in SeqAn:
     *
     * <li> @link BlastReport @endlink with the FormattedFile output specialization
     * @link BlastReportFileOut @endlink</li> <li> @link BlastTabular @endlink with
     * the FormattedFile output and input specializations @link BlastTabularFileOut
     * @endlink and @link BlastTabularFileIn @endlink</li> <li> @link BlastTabularLL
     * @endlink which provides light-weight, but very basic tabular IO </li>
     *
     * This is the third tag, it offers <b>low-level</b> support for reading and
     * writing NCBI Blast compatible <b>tabular</b> files, <b>without comment
     * lines</b> -- although files with comment lines can be read if the comment
     * lines are skipped. These are the formats that are available in legacy Blast
     * (<tt>blastall</tt> executable) with the parameters <tt>-m 8</tt> and <tt>-m
     * 9</tt> (with comment lines) and in BLAST+ (<tt>blastx</tt>,
     * <tt>blastn</tt>...) with the parameters <tt>-outfmt 6</tt> and <tt>-outfmt
     * 7</tt> respectively.
     *
     * For most situations @link BlastTabular @endlink is more adequate. Use this
     * tag's interface only for quick parsing of matches in a file, e.g counting and
     * filtering purposes. This interface does not offer a FormattedFile abstraction
     * and no convenience data structures, it does no transformations on the data.
     *
     * The reference Blast implementation used for developing the SeqAn support is
     * NCBI Blast+ 2.2.26 and NCBI Blast 2.2.26 for the legacy support.
     *
     * @section Input example
     *
     * The following example program extracts the list of matching query-subject-
     * pairs from a blast tabular file and prints it to std::out:
     *
     * @include demos/blast/blast_in_lowlevel.cpp
     *
     * The output looks like this:
     *
     * @include demos/blast/blast_in_lowlevel.cpp.stdout_
     *
     *
     *
     * @fn BlastTabularLL#onMatch
     *
     * @headerfile seqan/blast.h
     *
     * @brief Returns whether the iterator is on the beginning of a match line.
     *
     * @signature bool onMatch(stream, blastTabularLL)
     *
     * @param[in] iter An input iterator over a stream or any fwd-iterator over a
     *                 string.
     * @param[in] blastTabularLL The @link BlastTabularLL @endlink tag.
     *
     * @return bool true or false
     *
     * @throw IOError On low-level I/O errors.
     *
     * @fn BlastTabularLL#skipUntilMatch
     *
     * @headerfile seqan/blast.h
     *
     * @brief Skip arbitrary number of comment lines until the beginning of a match
     *        is reached.
     *
     * @signature void skipUntilMatch(stream, blastTabularLL);
     *
     * @param[in,out] stream An input iterator over a stream or any fwd-iterator
     *                       over a string.
     * @param[in] blastTabularLL The @link BlastTabularLL @endlink tag.
     *
     * @throw IOError On low-level I/O errors.
     * @throw ParseError On high-level file format errors.
     *
     * @section Remarks
     *
     * This is also part of the low-level IO and not required if you use readRecord.
     * Call this function whenever you are not @link BlastTabularLL#onMatch
     * @endlink, but want to be, e.g. to @link BlastTabularLL#readMatch @endlink.
     *
     * Since it is legal for files to end with comment lines, this function does not
     * throw if end-of-file is reached. You need to check that after calling.
     *
     * @fn BlastTabularLL#readMatch
     *
     * @headerfile seqan/blast.h
     *
     * @brief Low-level BlastTabular file reading.
     *
     * @signature void readMatch(stream, blastTabularLL, args ...);
     *
     * @param[in,out] stream An input iterator over a stream or any fwd-iterator
     *                       over a string.
     * @param[in] blastTabularLL The @link BlastTabularLL @endlink tag.
     * @param[out] args Arbitrary typed variables able to hold the fields.
     *
     * @throw IOError On low-level I/O errors.
     * @throw ParseError On high-level file format errors.
     *
     * @section Remarks
     *
     * Use this signature only if you do not or cannot use @link BlastMatch
     * @endlinkes. You can specify any number of arguments that are expected to be
     * able to hold the values in the columns read, i.e. if you pass a double as
     * argument and the value in the column cannot be successfully cast to double,
     * an exception will be thrown. If you want to be on the safe side, you can pass
     * CharStrings and evaluate them in another way.
     *
     * You may specify less columns than are available in the file, all but the
     * first n will be discarded.
     *
     * No transformations are made on the data, e.g. the positions are still one-
     * indexed and flipped for reverse strand matches.
     *
     * See @link BlastTabularLL @endlink for an example of low-level IO.
     *
     * @fn BlastTabularLL#writeMatch
     *
     * @headerfile seqan/blast.h
     *
     * @brief Low-level file-writing for blast tabular formats
     *
     * @signature void writeMatch(stream, blastTabularLL, columns...)
     *
     * @param[in,out] stream The file to write to (FILE, fstream, @link
     *                       OutputStreamConcept @endlink ...).
     * @param[in] blastTabularLL The @link BlastTabularLL @endlink tag.
     * @param[in] columns ... Any number of printable parameters.
     *
     * @throw IOError On low-level I/O errors.
     *
     * @section Remarks
     *
     * This is a very leight-weight alternative to @link
     * BlastTabularFileOut#writeRecord @endlink. It doesn't require @link BlastMatch
     * @endlinkes, @link BlastRecord @endlinks or the use of @link FormattedFile
     * @endlink. It supports an arbitrary amount of and arbitrary typed columns to
     * be printed.
     *
     * Use this only if you do not require comment lines and you are prepared to do
     * all transformations on the data yourself, i.e. this function does none of the
     * match adjustments mentioned in @link BlastTabularFileOut#writeRecord
     * @endlink.
     */