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bow edited this page Jun 29, 2012
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This GitHub branch is the official Biopython source code repository. It was initially an automatically updated mirror of Biopython's CVS repository, but the project has "migrated entirely to Git":http://news.open-bio.org/news/2009/09/biopython-cvs-to-git-migration/ as of September 2009, and this is now the primary development repository. See our "main website":http://biopython.org/wiki/GitMigration for more information.
The purpose of this Wiki is to serve as a 'sandbox' for the future SearchIO documentation. For now, I will try to note the important points that should later be covered in the real documentation.
Outline:
- Main functions: parse, read, to_dict, index, index_db, convert, write
- Supported programs and formats
- Object model: QueryResult, Hit, HSP
- Other things to notice (coordinate base (0 instead of 1), dna vs protein search coordinates, ID and Desc behavior, shallow vs deep copies)
- Format-specific usage guide
- Contributing your parser
- Attributes of common objects (e.g. seq_len or acc)
- Custom parsing / writing behavior (e.g. parsing custom columns in blast-tab, writing PSL files with headers)
For each of the formats + programs below, we should mention:
- Which program flavor and version do we support (or we're sure is supported)
- The custom attributes present in that format (e.g. HSP.z_score in fasta-m10 or HSP.cluster_num in hmmer-tab)
- Custom behavior not covered by the main API (e.g. custom blast-tab nonstandard column parsing)
- Gotchas / tricks that could be useful
- blast-xml
- blast-tab
- blast-tabc
- blast-text
- blat-psl
- blat-pslx
- fasta-m10
- hmmer-text
- hmmer-tab
- hmmer-domtab (hmmscan-domtab, hmmsearch-domtab, phmmer-domtab)