summaryrefslogtreecommitdiffstats
AgeCommit message (Collapse)AuthorFilesLines
2010-03-30Added simple print routines as an exercise in navigating the NCBI object stru...masterDon Pellegrino1-0/+10
2010-03-30Added simple print routines as an exercise in navigating the NCBI object stru...Don Pellegrino11-0/+193
2010-03-28Added new load routines for meta-data.Don Pellegrino1-0/+4
2010-03-28Testing options for loading meta-data/features/Entrez into HDF5.Don Pellegrino4-0/+376
2010-03-28Testing the meta-data/feature/Entrez load.Don Pellegrino1-1/+13
2010-03-28Added script for setting environment variables in preparation forDon Pellegrino1-0/+14
configure on a Debian system.
2010-03-28Replaced with more generic env-debian.sh which should work on anyDon Pellegrino1-38/+0
Debian system.
2010-03-28Added dependency on the libxml2 library for XML parsing.Don Pellegrino1-0/+9
2010-03-05Modified to take the location of the exp004 directory from anDon Pellegrino4-14/+60
environment variable.
2010-03-04Added dependency on NCBI Toolkit.Don Pellegrino1-0/+3
2010-01-25Added MatAssembly commands to write the cached data to the matrix structure.Don Pellegrino1-0/+3
2010-01-25Added script to build against a custom PETSc build with HDF5 support.Don Pellegrino1-0/+38
2010-01-25Test of writing a sparse matrix to disk.Don Pellegrino1-0/+10
2010-01-25Modified to build using the copy of PETSc already installed on Cobalt.Don Pellegrino5-46/+65
2010-01-25Added the initialization of a sparse matrix to be used to track theDon Pellegrino6-24/+127
pairwise BLAST scores for all influenza sequences. Modified the Autoconf input so that libraries are automatically added to LIBS rather than manually in Makefile.am. Added the use of the PETSc API which is used for the sparse matrix implementation.
2010-01-24Added notes for doing a build on NCSA Cobalt. Using the Intel C Compiler bui...Don Pellegrino1-0/+24
2010-01-24Commented out loading the BLAST file as thing shouldn't have to be done again...Don Pellegrino1-4/+2
2010-01-24Added library dependencies iherited from use of HDF5 on NCBI Cobalt including...Don Pellegrino2-6/+8
2010-01-24Modified to load the blast scores from a text file into the HDF5 file.Don Pellegrino1-8/+45
2010-01-23Added routines for loading BLAST scores.Don Pellegrino2-0/+4
2010-01-23Modified to test loading BLAST scores.Don Pellegrino1-0/+13
2010-01-23Minimized the scope of sequence_data_field_names.Don Pellegrino1-3/+3
2010-01-23Routines to load the results of a BLAST run into the HDF5 file.Don Pellegrino5-0/+208
2010-01-21Removed unused status variable from check_h5_error function.Donald Pellegrino7-31/+35
2010-01-20Updated the diagram to reflect the recent implementations of the aggregator.Don Pellegrino1-0/+0
2010-01-19Ran GNU indent on the code and headers.Don Pellegrino10-93/+99
2010-01-19Cleaned up some of the documentation.Don Pellegrino1-4/+3
2010-01-19Updated the merge command to reflect the new table structure in the HDF5 file.Don Pellegrino1-9/+20
2010-01-19Program now fully uses an existing file. The load functions detectDon Pellegrino7-86/+201
their existing target tables and purge them if they exist or create them if they don't. The assign function will reuse existing type values by gi and write a new table that is aligned by gi with influenza.faa.
2010-01-19Removed debugging flag. GNU Autotools is setting default debuggingDon Pellegrino1-1/+1
(-g) and optimization flags (-O2) automatically. To override these exporting CFLAGS at ./configure time is necessary.
2010-01-19Updated to compile. Code fills a new table of type values however it does no...Don Pellegrino1-106/+163
2010-01-18Organzied the functions into assign, error, load and model subdirectories. C...Don Pellegrino22-71/+181
2010-01-18Added R history file to the ignore list.Don Pellegrino1-0/+1
2010-01-18Scratch for exploring the HDF5 file in R.Don Pellegrino1-5/+11
2010-01-18Added error handling for the case where a GI record is not found in the BLAST...Don Pellegrino1-16/+57
2010-01-18Implemented updator to calculate and assign protein type values toDon Pellegrino7-96/+188
records which do not have them. This is a re-entrant process that only updates missing records and skips quickly through existing records. In addition premature termination loses at most 999 records of work since every thousand records are written back to the file and flushed to disk. Still to do is to write and flush the last set of records in the final bin under 1000. Also refactored the sequence_data structure so that it can be shared between HDF5 reading and writing operations.
2010-01-18Beginning of implmentation to iterate through and existing HDF5 and add calcu...Don Pellegrino3-14/+59
2010-01-18Moved updating the HDF5 file to a separate driver.Don Pellegrino3-8/+43
2010-01-18Added loading of the influenza.faa file.Don Pellegrino4-8/+126
2010-01-18Ran GNU indent to format the code as per GNU coding conventions.Don Pellegrino13-148/+145
2010-01-17Added error checking routines. Added implementation ofDon Pellegrino12-13/+211
assign_protein_type tested against a single hard-coded sequence input. The next step is to iterate over all records in the HDF5 collection that don't have a type assigned and to assign a type value.
2010-01-16Updated the diagram to remove an aggregator function for converting the year ...Don Pellegrino1-0/+0
2010-01-16Added the assign_protein_type function declaration without implementation.Don Pellegrino1-0/+2
2010-01-16Added the assign_protein_type function declaration without implementation.Don Pellegrino2-0/+20
2010-01-16R worksheet to explore the data from the HDF5 file.Don Pellegrino1-0/+19
2010-01-16Modified to convert the year field from text to numeric during the load.Don Pellegrino1-9/+17
2010-01-16Annotated the inimplemented methods of aggregator. This serves as a todo lis...Don Pellegrino1-0/+0
2010-01-16Added thoughts on the value provided by the HDF5 container.Don Pellegrino1-19/+37
Consideration of the anlaytical tools to be used and their load features should be considered to determine if the HDF5 container adds any value. In general custom C programs should get value out of saving the results of reading and ASCII to binary conversion steps back out to HDF5.
2010-01-16Added function declaration for load_influenza_faa.Don Pellegrino4-3/+31
2010-01-16Implemented the loading of the influenza_aa.dat file. Tested byDon Pellegrino4-41/+145
comparing an export of the data from the HDF5 file and the original file.
[next]

Valid XHTML 1.0 Strict

Copyright © 2009 Don Pellegrino All Rights Reserved.