exp007 - Influenza Data Processing

Age	Commit message (Collapse)	Author	Files	Lines
2010-01-25	Added the initialization of a sparse matrix to be used to track the	Don Pellegrino	6	-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.
2010-01-24	Commented out loading the BLAST file as thing shouldn't have to be done again...	Don Pellegrino	1	-4/+2

2010-01-24	Added library dependencies iherited from use of HDF5 on NCBI Cobalt including...	Don Pellegrino	2	-6/+8

2010-01-24	Modified to load the blast scores from a text file into the HDF5 file.	Don Pellegrino	1	-8/+45

2010-01-23	Added routines for loading BLAST scores.	Don Pellegrino	2	-0/+4

2010-01-23	Modified to test loading BLAST scores.	Don Pellegrino	1	-0/+13

2010-01-23	Minimized the scope of sequence_data_field_names.	Don Pellegrino	1	-3/+3

2010-01-23	Routines to load the results of a BLAST run into the HDF5 file.	Don Pellegrino	5	-0/+208

2010-01-21	Removed unused status variable from check_h5_error function.	Donald Pellegrino	7	-31/+35

2010-01-19	Ran GNU indent on the code and headers.	Don Pellegrino	10	-93/+99

2010-01-19	Cleaned up some of the documentation.	Don Pellegrino	1	-4/+3

2010-01-19	Program now fully uses an existing file. The load functions detect	Don Pellegrino	7	-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.
2010-01-19	Removed debugging flag. GNU Autotools is setting default debugging	Don Pellegrino	1	-1/+1
	(-g) and optimization flags (-O2) automatically. To override these exporting CFLAGS at ./configure time is necessary.
2010-01-19	Updated to compile. Code fills a new table of type values however it does no...	Don Pellegrino	1	-106/+163

2010-01-18	Organzied the functions into assign, error, load and model subdirectories. C...	Don Pellegrino	22	-71/+181

2010-01-18	Added error handling for the case where a GI record is not found in the BLAST...	Don Pellegrino	1	-16/+57

2010-01-18	Implemented updator to calculate and assign protein type values to	Don Pellegrino	7	-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.
2010-01-18	Beginning of implmentation to iterate through and existing HDF5 and add calcu...	Don Pellegrino	3	-14/+59

2010-01-18	Moved updating the HDF5 file to a separate driver.	Don Pellegrino	3	-8/+43

2010-01-18	Added loading of the influenza.faa file.	Don Pellegrino	4	-8/+126

2010-01-18	Ran GNU indent to format the code as per GNU coding conventions.	Don Pellegrino	13	-148/+145

2010-01-17	Added error checking routines. Added implementation of	Don Pellegrino	12	-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.
2010-01-16	Added the assign_protein_type function declaration without implementation.	Don Pellegrino	1	-0/+2

2010-01-16	Added the assign_protein_type function declaration without implementation.	Don Pellegrino	2	-0/+20

2010-01-16	Modified to convert the year field from text to numeric during the load.	Don Pellegrino	1	-9/+17

2010-01-16	Added function declaration for load_influenza_faa.	Don Pellegrino	4	-3/+31

2010-01-16	Implemented the loading of the influenza_aa.dat file. Tested by	Don Pellegrino	4	-41/+145
	comparing an export of the data from the HDF5 file and the original file.
2010-01-15	Code compiles and creates an HDF5 file containing a table with one	Don Pellegrino	5	-0/+208
	record of influenza_aa.dat populated.