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Three new formats in Biopython 1.75
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@peterjc
peterjc committed Nov 7, 2019
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Expand Up @@ -76,7 +76,7 @@ SeqIO](http://bioperl.org/howtos/SeqIO_HOWTO) and
| 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. |
| fastq-solexa | 1.50 | 1.50 | 1.52 | 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. |
| fastq-illumina | 1.51 | 1.51 | 1.52 | 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. |
| gck | git | No | No | The native format used by [Gene Construction Kit](http://www.textco.com/gene-construction-kit.php). |
| gck | 1.75 | No | No | The native format used by [Gene Construction Kit](http://www.textco.com/gene-construction-kit.php). |
| 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. |
| 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). |
| imgt | 1.56 | 1.56 | 1.56 | This refers to the IMGT variant of the EMBL plain text file format. |
Expand All @@ -89,13 +89,13 @@ SeqIO](http://bioperl.org/howtos/SeqIO_HOWTO) and
| seqxml | 1.58 | 1.58 | No | Simple [sequence XML file format](http://seqxml.org). |
| sff | 1.54 | 1.54 | 1.54 | Standard Flowgram Format ([SFF](http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=formats%23sff)) binary files produced by Roche 454 and IonTorrent/IonProton sequencing machines. |
| sff-trim | 1.54 | No | 1.54 | Standard Flowgram Format applying the trimming listed in the file. |
| snapgene | git | No | No | The native format used by [SnapGene](https://www.snapgene.com/). |
| snapgene | 1.75 | No | No | The native format used by [SnapGene](https://www.snapgene.com/). |
| 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. |
| 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. |
| 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. |
| 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. |
| uniprot-xml | 1.56 | No | 1.56 | UniProt XML format, successor to the plain text Swiss-Prot format. |
| xdna | git | git | No | The native format used by Christian Marck's DNA Strider and [Serial Cloner](http://serialbasics.free.fr/Serial_Cloner.html). |
| xdna | 1.75 | 1.75 | No | The native format used by Christian Marck's DNA Strider and [Serial Cloner](http://serialbasics.free.fr/Serial_Cloner.html). |
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With `Bio.SeqIO` you can treat sequence alignment file formats just like
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