# Bio.SearchIO.BlastIO package

## Submodules

- Bio.SearchIO.BlastIO.blast_tab module
  - `BlastTabIndexer`
    - `BlastTabIndexer.__init__()`
    - `BlastTabIndexer.__iter__()`
    - `BlastTabIndexer.get_raw()`
    - `BlastTabIndexer.__abstractmethods__`
    - `BlastTabIndexer.__annotations__`
    - `BlastTabIndexer.__firstlineno__`
    - `BlastTabIndexer.__static_attributes__`
  - `BlastTabParser`
    - `BlastTabParser.__init__()`
    - `BlastTabParser.__iter__()`
    - `BlastTabParser.__firstlineno__`
    - `BlastTabParser.__static_attributes__`
  - `BlastTabWriter`
    - `BlastTabWriter.__init__()`
    - `BlastTabWriter.write_file()`
    - `BlastTabWriter.__firstlineno__`
    - `BlastTabWriter.__static_attributes__`
- Bio.SearchIO.BlastIO.blast_xml module
  - `BlastXmlParser`
    - `BlastXmlParser.__init__()`
    - `BlastXmlParser.__iter__()`
    - `BlastXmlParser.__firstlineno__`
    - `BlastXmlParser.__static_attributes__`
  - `BlastXmlIndexer`
    - `BlastXmlIndexer.qstart_mark`
    - `BlastXmlIndexer.qend_mark`
    - `BlastXmlIndexer.block_size`
    - `BlastXmlIndexer.__init__()`
    - `BlastXmlIndexer.__iter__()`
    - `BlastXmlIndexer.get_raw()`
    - `BlastXmlIndexer.__abstractmethods__`
    - `BlastXmlIndexer.__annotations__`
    - `BlastXmlIndexer.__firstlineno__`
    - `BlastXmlIndexer.__static_attributes__`
  - `BlastXmlWriter`
    - `BlastXmlWriter.__init__()`
    - `BlastXmlWriter.write_file()`
    - `BlastXmlWriter.__firstlineno__`
    - `BlastXmlWriter.__static_attributes__`

## Module contents

Bio.SearchIO support for BLAST+ output formats.

This module adds support for parsing BLAST+ outputs. BLAST+ is a rewrite of NCBI’s legacy BLAST (Basic Local Alignment Search Tool), based on the NCBI C++ toolkit. The BLAST+ suite is available as command line programs or on NCBI’s web page.

Bio.SearchIO.BlastIO was tested on the following BLAST+ flavors and versions:

> - flavors: blastn, blastp, blastx, tblastn, tblastx

> - versions: 2.2.22+, 2.2.26+

You should also be able to parse outputs from a local BLAST+ search or from NCBI’s web interface. Although the module was not tested against all BLAST+, it should still be able to parse these other versions’ outputs. Please submit a bug report if you stumble upon an unparsable file.

Some output formats from the BLAST legacy suite (BLAST+’s predecessor) may still be parsed by this module. However, results are not guaranteed. You may try to use the Bio.Blast module to parse them instead.

More information about BLAST are available through these links:

  - Publication: http://www.biomedcentral.com/1471-2105/10/421

  - Web interface: http://blast.ncbi.nlm.nih.gov/

  - User guide: http://www.ncbi.nlm.nih.gov/books/NBK1762/

### Supported Formats

Bio.SearchIO.BlastIO supports the following BLAST+ output formats:

> - XML - ‘blast-xml’ - parsing, indexing, writing

> - Tabular - ‘blast-tab’ - parsing, indexing, writing

### blast-xml

The blast-xml parser follows the BLAST XML DTD written here: http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.mod.dtd

It provides the following attributes for each SearchIO object:

Object | Attribute | XML Element
--- | --- | ---
QueryResult | target | BlastOutput_db
program | BlastOutput_program
reference | BlastOutput_reference
version | BlastOutput_version [1]
description | Iteration_query-def
id | Iteration_query-ID
seq_len | Iteration_query-len
param_evalue_threshold | Parameters_expect
param_entrez_query | Parameters_entrez-query
param_filter | Parameters_filter
param_gap_extend | Parameters_gap-extend
param_gap_open | Parameters_gap-open
param_include | Parameters_include
param_matrix | Parameters_matrix
param_pattern | Parameters_pattern
param_score_match | Parameters_sc-match
param_score_mismatch | Parameters_sc-mismatch
stat_db_num | Statistics_db-num
stat_db_len | Statistics_db-len
stat_eff_space | Statistics_eff-space
stat_entropy | Statistics_entropy
stat_hsp_len | Statistics_hsp-len
stat_kappa | Statistics_kappa
stat_lambda | Statistics_lambda
Hit | accession | Hit_accession
description | Hit_def
id | Hit_id
seq_len | Hit_len
HSP | bitscore | Hsp_bit-score
density | Hsp_density
evalue | Hsp_evalue
gap_num | Hsp_gaps
ident_num | Hsp_identity
pos_num | Hsp_positive
bitscore_raw | Hsp_score
HSPFragment (also via HSP) | aln_span | Hsp_align-len
hit_frame | Hsp_hit-frame
hit_start | Hsp_hit-from
hit_end | Hsp_hit-to
hit | Hsp_hseq
aln_annotation | Hsp_midline
pattern_start | Hsp_pattern-from
pattern_end | Hsp_pattern-to
query_frame | Hsp_query-frame
query_start | Hsp_query-from
query_end | Hsp_query-to
query | Hsp_qseq

You may notice that in BLAST XML files, sometimes BLAST replaces your true sequence ID with its own generated ID. For example, the query IDs become ‘Query_1’, ‘Query_2’, and so on. While the hit IDs sometimes become ‘gnl|BL_ORD_ID|1’, ‘gnl|BL_ORD_ID|2’, and so on. In these cases, BLAST lumps the true sequence IDs together with their descriptions.

The blast-xml parser is aware of these modifications and will attempt to extract the true sequence IDs out of the descriptions. So when accessing QueryResult or Hit objects, you will use the non-BLAST-generated IDs.

This behavior on the query IDs can be disabled using the ‘use_raw_query_ids’ parameter while the behavior on the hit IDs can be disabled using the ‘use_raw_hit_ids’ parameter. Both are boolean values that can be supplied to SearchIO.read or SearchIO.parse, with the default values set to ‘False’.

In any case, the raw BLAST IDs can always be accessed using the query or hit object’s ‘blast_id’ attribute.

The blast-xml write function also accepts ‘use_raw_query_ids’ and ‘use_raw_hit_ids’ parameters. However, note that the default values for the writer are set to ‘True’. This is because the writer is meant to mimic native BLAST result as much as possible.

### blast-tab

The default format for blast-tab support is the variant without comments (-m 6 flag). Commented BLAST tabular files may be parsed, indexed, or written using the keyword argument ‘comments’ set to True:

    >>> # blast-tab defaults to parsing uncommented files
    >>> from Bio import SearchIO
    >>> uncommented = 'Blast/tab_2226_tblastn_004.txt'
    >>> qresult = SearchIO.read(uncommented, 'blast-tab')
    >>> qresult
    QueryResult(id='gi|11464971:4-101', 5 hits)

    >>> # set the keyword argument to parse commented files
    >>> commented = 'Blast/tab_2226_tblastn_008.txt'
    >>> qresult = SearchIO.read(commented, 'blast-tab', comments=True)
    >>> qresult
    QueryResult(id='gi|11464971:4-101', 5 hits)

For uncommented files, the parser defaults to using BLAST’s default column ordering: ‘qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore’.

If you want to parse an uncommented file with a customized column order, you can use the ‘fields’ keyword argument to pass the custom column order. The names of the column follow BLAST’s naming. For example, ‘qseqid’ is the column for the query sequence ID. These names may be passed either as a Python list or as a space-separated strings.

    >>> # pass the custom column names as a Python list
    >>> fname = 'Blast/tab_2226_tblastn_009.txt'
    >>> custom_fields = ['qseqid', 'sseqid']
    >>> qresult = next(SearchIO.parse(fname, 'blast-tab', fields=custom_fields))
    >>> qresult
    QueryResult(id='gi|16080617|ref|NP_391444.1|', 3 hits)

    >>> # pass the custom column names as a space-separated string
    >>> fname = 'Blast/tab_2226_tblastn_009.txt'
    >>> custom_fields = 'qseqid sseqid'
    >>> qresult = next(SearchIO.parse(fname, 'blast-tab', fields=custom_fields))
    >>> qresult
    QueryResult(id='gi|16080617|ref|NP_391444.1|', 3 hits)

You may also use the ‘std’ field name as an alias to BLAST’s default 12 columns, just like when you run a command line BLAST search.

Note that the ‘fields’ keyword argument will be ignored if the parsed file is commented. Commented files have their column ordering stated explicitly in the file, so there is no need to specify it again in SearchIO.

‘comments’ and ‘fields’ keyword arguments are both applicable for parsing, indexing, and writing.

blast-tab provides the following attributes for each SearchIO objects:

Object | Attribute | Column name
--- | --- | ---
QueryResult | accession | qacc
accession_version | qaccver
gi | qgi
seq_len | qlen
id | qseqid
Hit | accession | sacc
accession_version | sacc_ver
gi | sgi
gi_all | sallgi
id_all | sallseqid
seq_len | slen
id | sseqid
HSP | bitscore | bitscore
btop | btop
evalue | evalue
gapopen_num | gapopen
gap_num | gaps
ident_num | nident
ident_pct | pident
mismatch_num | mismatch
pos_pct | ppos
pos_num | positive
bitscore_raw | score
HSPFragment (also via HSP) | frames | frames [2]
aln_span | length
query_end | qend
query_frame | qframe
query | qseq
query_start | qstart
hit_end | send
hit_frame | sframe
hit | sseq
hit_start | sstart

If the parsed file is commented, the following attributes may be available as well:

Object | Attribute | Value
--- | --- | ---
QueryResult | description | query description
fields | columns in the output file
program | BLAST flavor
rid | remote search ID
target | target database
version | BLAST version

[1]

may be modified

[2]

When ‘frames’ is present, both `query_frame` and `hit_frame` will be present as well. It is recommended that you use these instead of ‘frames’ directly.

Biopython v: 1.85

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