Man pages for gschofl/blastr
A wrapper for NCBI Blast
| blast_db.sql | Load SQL schema for blast_db |
| BlastHeader-class | Class '"BlastHeader"' |
| blastn | Wrapper for the NCBI Nucleotide-Nucleotide BLAST |
| blastp | Wrapper for the NCBI Protein-Protein BLAST |
| BlastParameters-class | Class '"BlastParameters"' |
| blastr | A wrapper around NCBI Blast. |
| blastReport | Parse NCBI BLAST XML files. |
| BlastReport-class | Class '"BlastReport"' |
| blastReportDB | Parse NCBI BLAST XML files into BlastReportDB objects. |
| BlastReportDB-class | Class '"blastReportDB"' |
| blastTable | Parse NCBI BLAST table files into BlastTable objects. |
| BlastTable-class | Class '"BlastTable"' |
| blastx | Wrapper for the NCBI Translated Query-Protein Subject BLAST |
| coordinates | Access components of High-Scoring Pairs (HSPs) |
| db_bulk_insert | Insert a 'data.frame' into a corresponding SQLite table |
| db_connect | Connect to an existing SQLite database. |
| db_count | Count rows in a db table |
| db_create | Create an SQLite database. |
| db_disconnect | Disconnect from an SQLite database. |
| db_info | Metadata for an SQLite database. |
| db_is_current | Is a connection to an SQLite database still current. |
| db_list_fields | List available tables in an SQLite database |
| db_list_tables | List available tables in an SQLite database |
| db_query | Query an SQLite database. |
| Defline-class | Class '"Defline"' |
| Deflines | Parse fasta definition lines |
| DeflineSet-class | Class '"DeflineSet"' of '"Defline"' objects |
| do_log | Log a message to stderr. |
| dot_blast | Wrapper for the new NCBI BLAST+ tools |
| getAccession | Access components of BLAST Hits |
| getAlignLen | Access components of High-Scoring Pairs (HSPs) |
| getDefline | Access components of BLAST Hits |
| getGaps | Access components of High-Scoring Pairs (HSPs) |
| getGeneID | Access components of BLAST Hits |
| getHeader | Extract the header of a BLAST report |
| getHit | Access components of BLAST Queries |
| getHitCoverage | Extract the total Hit Coverage. |
| getHitDef | Access components of BLAST Hits |
| getHitID | Access components of BLAST Hits |
| getHitLen | Access components of BLAST Hits |
| getHitNum | Access components of BLAST Hits |
| getHsp | Access components of BLAST Hits |
| getHspHitID | Access components of BLAST Hits |
| getHspID | Access components of BLAST Hits |
| getHspNum | Access components of High-Scoring Pairs (HSPs) |
| getIdentity | Access components of High-Scoring Pairs (HSPs) |
| getParams | Extract parameters and statistics from a BLAST report |
| getPercGaps | Access components of High-Scoring Pairs (HSPs) |
| getPercIdentity | Access components of High-Scoring Pairs (HSPs) |
| getPercPositive | Access components of High-Scoring Pairs (HSPs) |
| getPositive | Access components of High-Scoring Pairs (HSPs) |
| getQuery | Extract queries from a BLAST report |
| getQueryCoverage | Extract the total Query Coverage. |
| getQueryDef | Access components of BLAST Queries |
| getQueryID | Access components of BLAST Queries |
| getQueryLen | Access components of BLAST Queries |
| getQueryNum | Access components of BLAST Queries |
| has_command | Test if an external executable is available |
| has_tables | Check if a SQLite database has specified tables |
| Hit-class | Class '"Hit"' |
| HitList-class | Class '"HitList"' of '"Hit"' objects |
| Hsp-class | Class '"Hsp"' |
| HspList-class | Class '"HspList"' of '"Hsp"' objects |
| linebreak | Format paragraphs |
| makeblasttdb | Wrapper for NCBI makeblastdb |
| make_deflines | Construct deflines |
| nhits | Access components of BLAST Queries |
| nhsps | Access components of BLAST Hits |
| qblast | Do a BLAST search using the QBLAST URL API |
| Query-class | Class '"Query"' |
| QueryList-class | Class '"QueryList"' of '"Query"' objects |
| rpsblast | Wrapper for the NCBI Reversed Position Specific Blast |
| scores | Access components of High-Scoring Pairs (HSPs) |
| sequence | Access components of High-Scoring Pairs (HSPs) |
| SQLiteDB-class | Class '"SQLiteDB"' |
| SysCall | Wrapper for system commands |
| tblastn | Wrapper for the NCBI Protein Query-Translated Subject BLAST |
| tblastx | Wrapper for the NCBI Translated Query-Protein Subject BLAST |
| timestamp | Generate a timestamp string. |
| update_blastdb | Wrapper for 'update_blastdb' |
