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MarkusPiotrowskiMarkusPiotrowski
committedMay 8, 2016
Seq pages and others, small corrections, updated links etc.
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‎wiki/Remove_PDB_disordered_atoms.md

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Solution
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--------
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[`Bio.PDB`](http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc118)
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[`Bio.PDB`](http://biopython.org/DIST/docs/tutorial/Tutorial.html)
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is proficient in dealing with disordered atoms. Each disordered atom has
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a property indicating its alternative positions: `atom.altloc`. Usually
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there are only two alternative positions labelled *'A'* and *'B'*. The key

‎wiki/Scriptcentral.md

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‎wiki/SearchIO.md

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---
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title: SearchIO
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title: Introduction to SearchIO
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permalink: wiki/SearchIO
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layout: wiki
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tags:
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- Wiki Documentation
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---
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Matching the names in BioPerl, Biopython has a [SeqIO](SeqIO "wikilink")
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module for sequence file input/output, and [AlignIO](AlignIO "wikilink")
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Matching the names in BioPerl, Biopython has a [`SeqIO`](SeqIO "wikilink")
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module for sequence file input/output, and [`AlignIO`](AlignIO "wikilink")
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for multiple sequence alignment input/output. The third member of the
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BioPerl trio is SearchIO, and a Biopython equivalent was written during
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summer 2012 by [Google Summer of Code](Google_Summer_of_Code "wikilink")
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student Wibowo Arindrarto ([blog](http://bow.web.id/blog/2012/08/back-on-the-main-branch/)).
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This covers pairwise sequence search file input/output, for example from
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BLAST, HMMER, BLAT, or Bill Pearson's FASTA suite. See the [BioPerl
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SearchIO HOWTO](http://www.bioperl.org/wiki/HOWTO:SearchIO) for
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SearchIO HOWTO](http://bioperl.org/howtos/SearchIO_HOWTO.html) for
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background.
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It is included in Biopython 1.61 onwards as an *experimental* module if
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you want to test it. An chapter in the
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you want to test it. A chapter in the
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[Tutorial](http://biopython.org/DIST/docs/tutorial/Tutorial.html)
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([PDF](http://biopython.org/DIST/docs/tutorial/Tutorial.pdf)) on
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Bio.SearchIO is also published alongside the 1.61 release.
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`Bio.SearchIO` is also published alongside the 1.61 release.
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This wiki describes the important bits with some small examples. For a
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full reference, consult the [API
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Supported File Formats
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----------------------
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The table below lists all formats supported by Bio.SearchIO. Note that
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The table below lists all formats supported by `Bio.SearchIO`. Note that
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for writing support, the writer assumes that all the necessary
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attributes of the objects being written are present. It is not possible,
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for example, to write BLAST XML data to a HMMER 3.0 plain text output
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straight away.
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<table style="width:100%;">
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<caption>Table 1: Bio.SearchIO supported file formats</caption>
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<colgroup>
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<col width="12%" />
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<col width="22%" />
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<col width="22%" />
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<col width="22%" />
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<col width="22%" />
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</colgroup>
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<thead>
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<tr class="header">
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<th><p>Format name</p></th>
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<th><p>Read</p></th>
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<th><p>Write</p></th>
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<th><p>Index</p></th>
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<th><p>Notes</p></th>
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</tr>
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</thead>
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<tbody>
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<tr class="odd">
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<td><p>blast-tab</p></td>
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<td><p>1.61</p></td>
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<td><p>1.61</p></td>
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<td><p>1.61</p></td>
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<td><p>BLAST+ tabular output (both <code>-m</code> <code>6</code> and <code>-m</code> <code>7</code> flags are supported).</p></td>
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</tr>
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<tr class="even">
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<td><p>blast-text</p></td>
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<td><p>1.61</p></td>
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<td><p>n/a</p></td>
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<td><p>n/a</p></td>
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<td><p>BLAST+ plain text output (up to version 2.2.26+). Newer versions may not always work.</p></td>
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</tr>
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<tr class="odd">
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<td><p>blast-xml</p></td>
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<td><p>1.61</p></td>
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<td><p>1.61</p></td>
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<td><p>1.61</p></td>
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<td><p>BLAST+ XML output.</p></td>
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</tr>
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<tr class="even">
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<td><p>blat-psl</p></td>
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<td><p>1.61</p></td>
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<td><p>1.61</p></td>
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<td><p>1.61</p></td>
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<td><p>BLAT default output (PSL format). Variants with or without header are both supported. PSLX (PSL + sequences) is also supported.</p></td>
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</tr>
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<tr class="odd">
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<td><p>exonerate-text</p></td>
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<td><p>1.61</p></td>
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<td><p>n/a</p></td>
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<td><p>1.61</p></td>
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<td><p>Exonerate plain text output. Due to the way Biopython stores its sequences, at the moment support is limited to text outputs without split codons (for protein queries). If you are parsing a text output of protein queries containing split codon alignments (for example, from the <code>protein2genome</code> alignment mode), the parser will fail.</p></td>
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</tr>
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<tr class="even">
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<td><p>exonerate-cigar</p></td>
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<td><p>1.61</p></td>
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<td><p>n/a</p></td>
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<td><p>1.61</p></td>
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<td><p>Exonerate cigar string.</p></td>
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</tr>
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<tr class="odd">
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<td><p>exonerate-vulgar</p></td>
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<td><p>1.61</p></td>
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<td><p>n/a</p></td>
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<td><p>1.61</p></td>
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<td><p>Exonerate vulgar string.</p></td>
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</tr>
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<tr class="even">
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<td><p>fasta-m10</p></td>
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<td><p>1.61</p></td>
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<td><p>n/a</p></td>
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<td><p>1.61</p></td>
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<td><p>Bill Pearson's FASTA <code>-m</code> <code>10</code> output.</p></td>
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</tr>
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<tr class="odd">
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<td><p>hmmer3-domtab</p></td>
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<td><p>1.61</p></td>
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<td><p>1.61</p></td>
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<td><p>1.61</p></td>
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<td><p>HMMER3.0 domain table output format. The name <code>hmmer3-domtab</code> per se is in fact not used, since the program name has to be specified. For example, when parsing hmmscan output, the format name would be <code>hmmscan-domtab</code>.</p></td>
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</tr>
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<tr class="even">
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<td><p>hmmer3-tab</p></td>
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<td><p>1.61</p></td>
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<td><p>1.61</p></td>
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<td><p>1.61</p></td>
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<td><p>HMMER 3.0 table output format.</p></td>
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</tr>
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<tr class="odd">
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<td><p>hmmer3-text</p></td>
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<td><p>1.61</p></td>
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<td><p>n/a</p></td>
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<td><p>1.61</p></td>
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<td><p>HMMER 3.0 plain text output format.</p></td>
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</tr>
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<tr class="even">
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<td><p>hmmer2-text</p></td>
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<td><p>1.61</p></td>
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<td><p>n/a</p></td>
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<td><p>1.61</p></td>
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<td><p>HMMER 2.x plain text output format.</p></td>
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</tr>
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<tr class="odd">
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</tr>
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</tbody>
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</table>
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|Format name |Read |Write|Index| Notes |
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|---------------|-----|-----|-----|------------------------------------|
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|blast-tab |1.61 |1.61 |1.61 |BLAST+ tabular output (both `-m 6` and `-m 7` flags are supported).|
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|blast-text |1.61 |n/a |n/a |BLAST+ plain text output (up to version 2.2.26+). Newer versions may not always work.|
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|blast-xml |1.61 |1.61 |1.61 |BLAST+ XML output. |
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|blat-psl |1.61 |1.61 |1.61 |BLAT default output (PSL format). Variants with or without header are both supported. PSLX (PSL + sequences) is also supported.|
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|exonerate-text |1.61 |n/a |1.61 |Exonerate plain text output. Due to the way Biopython stores its sequences, at the moment support is limited to text outputs without split codons (for protein queries). If you are parsing a text output of protein queries containing split codon alignments (for example, from the `protein2genome` alignment mode), the parser will fail.|
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exonerate-cigar |1.61 |n/a |1.61 |Exonerate cigar string. |
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exonerate-vulgar|1.61 |n/a |1.61 |Exonerate vulgar string. |
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fasta-m10 |1.61 |n/a |1.61 |Bill Pearson's FASTA `-m 10` output.|
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hmmer3-domtab |1.61 |1.61 |1.61 |HMMER3.0 domain table output format. The name `hmmer3-domtab` per se is in fact not used, since the program name has to be specified. For example, when parsing hmmscan output, the format name would be `hmmscan-domtab`.|
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hmmer3-tab |1.61 |1.61 |1.61 |HMMER 3.0 table output format. |
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hmmer3-text |1.61 |n/a |1.61 |HMMER 3.0 plain text output format. |
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hmmer2-text |1.61 |n/a |1.61 |HMMER 2.x plain text output format. |
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Format-specific Arguments
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-------------------------
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Although mostly similar to Biopython's SeqIO and AlignIO modules, there
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is a small difference in the main Bio.SearchIO functions. Depending on
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Although mostly similar to Biopython's `SeqIO` and `AlignIO` modules, there
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is a small difference in the main `Bio.SearchIO` functions. Depending on
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the file format being used, you may pass additional keyword arguments
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that determines how the parser / indexer / writer behaves. Shown below
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are some formats which accepts extra keyword arguments.
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| Format name | Argument name | Default value | Applicable for | Explanation |
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|-------------|------------------------------------------|----------------------------|---------------------------------------------------------------------------------------------|-------------------------------------------------------------------------|
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| blast-tab | comments | False | reading, writing, indexing | Boolean, whether the input/output file is the commented variant or not. |
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| fields | Default BLAST tabular output field names | reading, writing, indexing | Space-separated string, list of fields / columns in the input/output file. |
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| blast-xml | encoding | "utf-8" | writing | XML encoding name. |
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| indent | " " (empty space) | writing | Character(s) to use for indenting the XML. |
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| increment | 2 | writing | How many times the character defined in `indent` are printed when printing a child element. |
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| blat-psl | pslx | False | reading, writing, indexing | Boolean, whether the input/output file contains sequences or not. |
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| blast-tab | comments | False | Reading, writing, indexing | Boolean, whether the input/output file is the commented variant or not. |
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| fields | Default BLAST tabular output field names | reading, writing, indexing | Space-separated string, list of fields / columns in the input/output file. | |
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| blast-xml | encoding | "utf-8" | Writing | XML encoding name. |
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| indent | " " (empty space) | writing | Character(s) to use for indenting the XML. | |
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| increment | 2 | writing | How many times the character defined in `indent` are printed when printing a child element. | |
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| blat-psl | pslx | False | Reading, writing, indexing | Boolean, whether the input/output file contains sequences or not. |
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| header | False | writing | Boolean, whether to write PSL header or not. |
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||
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Conventions
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-----------
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The main goal of creating Bio.SearchIO is to have a common, easy to use
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The main goal of creating `Bio.SearchIO` is to have a common, easy to use
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interface across different search output files. As such, we have also
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created some conventions / standards for Bio.SearchIO that extend beyond
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created some conventions / standards for `Bio.SearchIO` that extend beyond
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the common object model. These conventions apply to all files parsed by
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Bio.SearchIO, regardless of their individual formats.
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`Bio.SearchIO`, regardless of their individual formats.
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### Python-style sequence coordinates
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When storing sequence coordinates (start and end values), Bio.SearchIO
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When storing sequence coordinates (start and end values), `Bio.SearchIO`
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uses the Python-style slice convention: zero-based and half-open
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intervals. For example, if in a BLAST XML output file the start and end
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coordinates of an HSP are 10 and 28, they would become 9 and 28 in
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Bio.SearchIO. The start coordinate becomes 9 because Python indices
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`Bio.SearchIO`. The start coordinate becomes 9 because Python indices
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start from zero, while the end coordinate remains 28 as Python slices
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omit the last item in an interval.
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in the database hit.
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When these objects are written to an output file using
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Bio.SearchIO.write, the coordinate values are restored to their
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`Bio.SearchIO.write`, the coordinate values are restored to their
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respective format's convention. Using the example above, if the HSP
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would be written to an XML file, the start and end coordinates would
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become 10 and 28 again.
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plain text format if the matching strand lies in the minus orientation,
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then the start coordinate will always be bigger than the end coordinate.
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In Bio.SearchIO, start coordinates are always smaller than the end
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In `Bio.SearchIO`, start coordinates are always smaller than the end
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coordinates, regardless of their originating strand. This ensures
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consistency when using the coordinates to slice full sequences.
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Similar to the coordinate style convention, the start and end
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coordinates' order are restored to their respective formats when the
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objects are written using Bio.SearchIO.write.
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objects are written using `Bio.SearchIO.write`.
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### Frames and strand values
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Bio.SearchIO only allows -1, 0, 1 and None as strand values. For frames,
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the only allowed values are integers from -3 to 3 (inclusive) and None.
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`Bio.SearchIO` only allows *-1*, *0*, *1* and `None` as strand values. For frames,
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the only allowed values are integers from -3 to 3 (inclusive) and `None`.
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Both of these are standard Biopython conventions.
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FAQ
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---
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- *How does Bio.SearchIO differ from Bio.Blast.NCBIXML*?
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- *How does `Bio.SearchIO` differ from `Bio.Blast.NCBIXML`*?
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Both modules are based on completely different object models and are
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not compatible with each other. Not only that, the underlying
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parsers and writers are also different (indexing is not possible
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with Bio.Blast.NCBIXML). Finally, Bio.SearchIO is planned to be the
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replacement of Bio.Blast.NCBIXML.
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with `Bio.Blast.NCBIXML`). Finally, `Bio.SearchIO` is planned to be the
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replacement of `Bio.Blast.NCBIXML`.
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<!-- -->
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- *How does Bio.SearchIO differ from Bio.Blast.NCBIStandalone*?
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Again, they provide different object models. However, Bio.SearchIO
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currently uses the parser from Bio.Blast.NCBIStandalone internally,
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but that old module will be deprecated.
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- *How does `Bio.SearchIO` differ from `Bio.Blast.NCBIStandalone`*?
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Again, they provide different object models. However, `Bio.SearchIO`
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currently uses the parser from `Bio.Blast.NCBIStandalone` internally,
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but that old module will be deprecated.

‎wiki/Seq.md

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---
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title: Seq
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title: The Seq Object
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permalink: wiki/Seq
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layout: wiki
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tags:
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- Wiki Documentation
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---
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In Biopython, sequences are usually held as **Seq** objects, which hold
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In Biopython, sequences are usually held as ` Seq` objects, which hold
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the sequence string and an associated alphabet.
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This page describes the Biopython **Seq** object, defined in the Bio.Seq
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module (together with related objects like the **MutableSeq**, plus some
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This page describes the Biopython `Seq` object, defined in the `Bio.Seq`
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module (together with related objects like the `MutableSeq`, plus some
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general purpose sequence functions). In addition to this wiki page,
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there is a whole chapter in the
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[Tutorial](http://biopython.org/DIST/docs/tutorial/Tutorial.html)
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([PDF](http://biopython.org/DIST/docs/tutorial/Tutorial.pdf)) on the
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**Seq** object - plus its [API
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`Seq` object - plus its [API
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documentation](http://biopython.org/DIST/docs/api/Bio.Seq.Seq-class.html)
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(which you can read online, or from within Python with the help
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command).
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If you need to store additional information like a sequence identifier
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or name, or even more details like a description or annotation, then we
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use a [SeqRecord](SeqRecord "wikilink") object instead. These are the
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sequence records used by the [SeqIO](SeqIO "wikilink") module for
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use a [`SeqRecord`](SeqRecord "wikilink") object instead. These are the
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sequence records used by the [`SeqIO`](SeqIO "wikilink") module for
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reading and writing sequence files.
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The Seq Object
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==============
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The Seq object essentially combines a Python string with an (optional)
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The `Seq` object essentially combines a Python string with an (optional)
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biological alphabet. For example:
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``` python
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In the above example, we haven't specified an alphabet so we end up with
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a default generic alphabet. Biopython doesn't know if this is a
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nucleotide sequence or a protein rich in alanines, glycines, cysteines
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and threonines. If you know, you should supply this information:
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and threonines. If *you* know, you should supply this information:
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``` python
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>>> from Bio.Seq import Seq
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Why is this important? Well it can catch some errors for you - you
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wouldn't want to accidentally try and combine a DNA sequence with a
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protein would you:
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protein, would you?
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``` python
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>>> my_protein + my_dna
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General methods
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---------------
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The Seq object has a number of methods which act just like those of a
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The `Seq` object has a number of methods which act just like those of a
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Python string, for example the find method:
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``` python
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### Complement and reverse complement
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These are very simple - the methods return a new Seq object with the
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These are very simple - the methods return a new `Seq` object with the
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appropriate sequence and the same alphabet:
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``` python
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ValueError: Proteins do not have complements!
249249
```
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You can use them on Seq objects with a generic alphabet:
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You can use them on `Seq` objects with a generic alphabet:
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``` python
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>>> my_seq.complement()

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