BLAST Control Module
Copyright © 2005 Richard J. Edwards - See source code for GNU License Notice
Performs BLAST searches and loads results into objects. Peforms GABLAM conversion of local alignments into global
alignment statistics. Remember to set
BLASTRun = Full BLAST run
History Module Version History
# 0.0 - Initial Working Compilation. # 0.1 - No Out Object in Objects # 1.0 - Corrected to work with blastn (and blastp) # 1.1 - Added special calling for Cerberus # 1.2 - Added GABLAM and GABLAMO to BlastHit # 1.3 - Added GABLAM calculation upon reading BLAST results and clearing Alignment sequences to save memory # 1.4 - Tidied up the module with improved logging and progress reporting. Added dbCleanup. # 1.5 - Added checking for multiple hits with same name and modified BLAST_Run.hitToSeq() # 1.6 - Added nucleotide vs protein searches to GABLAM # 1.7 - Added nucleotide vs nucleotide searches to GABLAM # 1.8 - Added local alignment summary output to ReadBLAST() # 1.9 - Added BLAST -C # 1.10- Added BLAST -g # 1.11- Added gablamfrag=X : Length of gaps between mapped residue for fragmenting local hits  # 1.12- Altered checkDB and cleanupDB to spot index files split over multiple files (*.00.p* etc.) # 1.13- Added localcut=X : Cut-off length for local alignments contributing to global GABLAM stats)  # 1.14- Added blast.checkProg(qtype,stype) to check whether blastp setting matches sequence formats. # 1.15- Added OldBLAST/Legacy option to Object for compatibility with rje_blast_V2. (Always True!)
rje_blast REST Output formatsThe standard REST call is in the form:
will be parsed into summary tables. If
each query with its hits. Each local alignment is a separate sequence in the alignment unless
used to convert QAssemble alignments to consensus sequences.
a tie, the query sequence is used if it's one of the options, else the highest ranked one is used.
which is formatted as follows:
###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~### # OUTFMT: ... contents for OUTFMT section ...
After running, click on the
file will usually also be output:
Available REST Outputs
NOTE: If run in
query will have QAssembly output in the
qassembly alignment, named after their accession numbers.
© 2015 RJ Edwards. Contact: email@example.com.