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peterjcpeterjc
committedApr 24, 2016
Update links to bioperl.org website.
See #17 for fixing the old inter-wiki links.
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‎wiki/SeqIO.md

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@@ -33,10 +33,10 @@ objects. There is a sister interface [Bio.AlignIO](AlignIO "wikilink")
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for working directly with sequence alignment files as Alignment objects.
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The design was partly inspired by the simplicity of [BioPerl's
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SeqIO](bp:HOWTO:SeqIO "wikilink"). In the long term we hope to match
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SeqIO](http://bioperl.org/howtos/SeqIO_HOWTO). In the long term we hope to match
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BioPerl's impressive list of supported [sequence file
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formats](bp:Sequence_formats "wikilink") and [multiple alignment
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formats](bp:Multiple_alignment_formats "wikilink").
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formats](http://bioperl.org/formats/sequence_formats/) and [multiple alignment
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formats](http://bioperl.org/formats/alignment_formats/).
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Note that the inclusion of Bio.SeqIO (and
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[Bio.AlignIO](AlignIO "wikilink")) in Biopython does lead to some
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[git](git "wikilink") to indicate this is supported in our latest in
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development code). The format name is a simple lowercase string. Where
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possible we use the same name as [BioPerl's
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SeqIO](bp:HOWTO:SeqIO#Formats "wikilink") and
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SeqIO](http://bioperl.org/howtos/SeqIO_HOWTO) and
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[EMBOSS](http://emboss.sourceforge.net/docs/themes/SequenceFormats.html).
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| Format name | Read | Write | Index | Notes |
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|-----------------------|------|-------------|-------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| abi | 1.58 | No | N/A | Reads the ABI "Sanger" capillary sequence traces files, including the PHRED quality scores for the base calls. This allows ABI to FASTQ conversion. Note each ABI file contains one and only one sequence (so there is no point in indexing the file). |
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| ace | 1.47 | No | 1.52 | Reads the contig sequences from an ACE assembly file. Uses Bio.Sequencing.Ace internally |
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| clustal | 1.43 | 1.43 | No | The [alignment format of Clustal X and Clustal W](bp:ClustalW_multiple_alignment_format "wikilink"). |
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| embl | 1.43 | 1.54 | 1.52 | The [EMBL flat file format](bp:EMBL_sequence_format "wikilink"). Uses Bio.GenBank internally. |
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| fasta | 1.43 | 1.43 | 1.52 | This refers to the input [FASTA file format](bp:FASTA_sequence_format "wikilink") introduced for Bill Pearson's FASTA tool, where each record starts with a ">" line. Resulting sequences have a generic alphabet by default. |
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| clustal | 1.43 | 1.43 | No | The [alignment format of Clustal X and Clustal W](http://bioperl.org/formats/alignment_formats/ClustalW_multiple_alignment_format). |
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| embl | 1.43 | 1.54 | 1.52 | The [EMBL flat file format](http://bioperl.org/formats/sequence_formats/EMBL_sequence_format). Uses Bio.GenBank internally. |
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| fasta | 1.43 | 1.43 | 1.52 | This refers to the input [FASTA file format](http://bioperl.org/formats/sequence_formats/FASTA_sequence_format) introduced for Bill Pearson's FASTA tool, where each record starts with a ">" line. Resulting sequences have a generic alphabet by default. |
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| fastq-sanger or fastq | 1.50 | 1.50 | 1.52 | [FASTQ files](http://en.wikipedia.org/wiki/FASTQ_format) are a bit like FASTA files but also include sequencing qualities. In Biopython, "fastq" (or the alias "fastq-sanger") refers to Sanger style FASTQ files which encode PHRED qualities using an ASCII offset of 33. See also the incompatible "fastq-solexa" and "fastq-illumina" variants used in early Solexa/Illumina pipelines, Illumina pipeline 1.8 produces Sanger FASTQ. |
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| fastq-solexa | 1.50 | 1.50 | 1.52 | [FASTQ files](http://en.wikipedia.org/wiki/FASTQ_format) are a bit like FASTA files but also include sequencing qualities. In Biopython, "fastq-solexa" refers to the original Solexa/Illumina style FASTQ files which encode Solexa qualities using an ASCII offset of 64. See also what we call the "fastq-illumina" format. |
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| fastq-illumina | 1.51 | 1.51 | 1.52 | [FASTQ files](http://en.wikipedia.org/wiki/FASTQ_format) are a bit like FASTA files but also include sequencing qualities. In Biopython, "fastq-illumina" refers to early Solexa/Illumina style FASTQ files (from pipeline version 1.3 to 1.7) which encode PHRED qualities using an ASCII offset of 64. For *good* quality reads, PHRED and Solexa scores are approximately equal, so the "fastq-solexa" and "fastq-illumina" variants are almost equivalent. |
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| genbank or gb | 1.43 | 1.48 / 1.51 | 1.52 | The [GenBank or GenPept flat file format](bp:GenBank_sequence_format "wikilink"). Uses Bio.GenBank internally for parsing. Biopython 1.48 to 1.50 wrote basic GenBank files with only minimal annotation, while 1.51 onwards will also write the features table. |
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| ig | 1.47 | No | 1.52 | This refers to the IntelliGenetics file format, apparently the same as the [MASE alignment format](bp:Mase_multiple_alignment_format "wikilink"). |
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| genbank or gb | 1.43 | 1.48 / 1.51 | 1.52 | The [GenBank or GenPept flat file format](http://bioperl.org/formats/sequence_formats/GenBank_sequence_format). Uses Bio.GenBank internally for parsing. Biopython 1.48 to 1.50 wrote basic GenBank files with only minimal annotation, while 1.51 onwards will also write the features table. |
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| ig | 1.47 | No | 1.52 | This refers to the IntelliGenetics file format, apparently the same as the [MASE alignment format](http://bioperl.org/formats/alignment_formats/Mase_multiple_alignment_format). |
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| imgt | 1.56 | 1.56 | 1.56 | This refers to the IMGT variant of the EMBL plain text file format. |
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| nexus | 1.43 | 1.48 | No | The [NEXUS multiple alignment](bp:NEXUS_multiple_alignment_format "wikilink") format, also known as PAUP format. Uses Bio.Nexus internally. |
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| nexus | 1.43 | 1.48 | No | The [NEXUS multiple alignment](http://bioperl.org/formats/alignment_formats/NEXUS_multiple_alignment_format) format, also known as PAUP format. Uses Bio.Nexus internally. |
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| pdb-seqres | 1.61 | No | No | Reads a Protein Data Bank (PDB) file to determine the complete protein sequence as it appears in the header (no dependency on Bio.PDB and NumPy). |
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| pdb-atom | 1.61 | No | No | Uses Bio.PDB to determine the (partial) protein sequence as it appears in the structure based on the atom coordinate section of the file (requires NumPy). |
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| phd | 1.46 | 1.52 | 1.52 | [PHD files](bp:PHD_sequence_format "wikilink") are output from PHRED, used by PHRAP and CONSED for input. Uses Bio.Sequencing.Phd internally. |
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| phylip | 1.43 | 1.43 | No | An alignment format. Truncates names at 10 characters. |
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| pir | 1.48 | No | 1.52 | A "FASTA like" format introduced by the National Biomedical Research Foundation (NBRF) for the [Protein Information Resource (PIR)](bp:PIR_sequence_format "wikilink") database, now part of UniProt. |
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| phd | 1.46 | 1.52 | 1.52 | [PHD files](http://bioperl.org/formats/sequence_formats/PHD_sequence_format) are output from PHRED, used by PHRAP and CONSED for input. Uses Bio.Sequencing.Phd internally. |
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| phylip | 1.43 | 1.43 | No | [PHYLIP files](http://bioperl.org/formats/alignment_formats/PHYLIP_multiple_alignment_format). Truncates names at 10 characters. |
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| pir | 1.48 | No | 1.52 | A "FASTA like" format introduced by the National Biomedical Research Foundation (NBRF) for the [Protein Information Resource (PIR)](http://bioperl.org/formats/sequence_formats/PIR_sequence_format) database, now part of UniProt. |
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| seqxml | 1.58 | 1.58 | No | Simple [sequence XML file format](http://seqxml.org). |
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| sff | 1.54 | 1.54 | 1.54 | Standard Flowgram Format ([SFF](http://www.ncbi.nlm.nih.gov/books/NBK47537/#File_Format_Guide_B.Standard_Flowgram_Fo)) binary files produced by Roche 454 and IonTorrent/IonProton sequencing machines. |
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| stockholm | 1.43 | 1.43 | No | The [Stockholm alignment format](bp:Stockholm_multiple_alignment_format "wikilink") is also known as PFAM format. |
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| swiss | 1.43 | No | 1.52 | [Swiss-Prot](bp:Swissprot_sequence_format "wikilink") aka UniProt format. Uses Bio.SwissProt internally. See also the UniProt XML format. |
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| tab | 1.48 | 1.48 | 1.52 | [Simple two column tab separated sequence files](bp:Tab_sequence_format "wikilink"), where each line holds a record's identifier and sequence. For example, this is used by Aligent's eArray software when saving microarray probes in a minimal tab delimited text file. |
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| qual | 1.50 | 1.50 | 1.52 | [Qual files](bp:Qual_sequence_format "wikilink") are a bit like FASTA files but instead of the sequence, record space separated integer sequencing values as PHRED quality scores. A matched pair of FASTA and QUAL files are often used as an alternative to a single FASTQ file. |
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| stockholm | 1.43 | 1.43 | No | The [Stockholm alignment format](http://bioperl.org/formats/alignment_formats/Stockholm_multiple_alignment_format) is also known as PFAM format. |
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| swiss | 1.43 | No | 1.52 | [Swiss-Prot](http://bioperl.org/formats/sequence_formats/Swissprot_sequence_format) aka UniProt format. Uses Bio.SwissProt internally. See also the UniProt XML format. |
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| tab | 1.48 | 1.48 | 1.52 | [Simple two column tab separated sequence files](http://bioperl.org/formats/sequence_formats/Tab_sequence_format), where each line holds a record's identifier and sequence. For example, this is used by Aligent's eArray software when saving microarray probes in a minimal tab delimited text file. |
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| qual | 1.50 | 1.50 | 1.52 | [Qual files](http://bioperl.org/formats/sequence_formats/Qual_sequence_format) are a bit like FASTA files but instead of the sequence, record space separated integer sequencing values as PHRED quality scores. A matched pair of FASTA and QUAL files are often used as an alternative to a single FASTQ file. |
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| uniprot-xml | 1.56 | No | 1.56 | UniProt XML format, successor to the plain text Swiss-Prot format. |
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||
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file uses Unix, Mac or DOS/Windows style newline characters.
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Note that you *must* specify the file format explicitly, unlike
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[BioPerl's SeqIO](bp:HOWTO:SeqIO "wikilink") which can try to guess
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[BioPerl's SeqIO](http://bioperl.org/howtos/SeqIO_HOWTO) which can try to guess
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using the file name extension and/or the file contents. See *Explicit is
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better than implicit* ([The Zen of
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Python](http://www.python.org/dev/peps/pep-0020/)).

‎wiki/SeqIO_dev.md

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### KEGG format
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Can Bio.KEGG parse files in [KEGG
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format](bp:KEGG_sequence_format "wikilink")?
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format](http://bioperl.org/formats/sequence_formats/KEGG_sequence_format)?
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### MEME format
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