exp007 - Influenza Data Processing

Age	Commit message (Collapse)	Author	Files	Lines
2010-01-19	Updated the merge command to reflect the new table structure in the HDF5 file.	Don Pellegrino	1	-9/+20

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 R history file to the ignore list.	Don Pellegrino	1	-0/+1

2010-01-18	Scratch for exploring the HDF5 file in R.	Don Pellegrino	1	-5/+11

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	Updated the diagram to remove an aggregator function for converting the year ...	Don Pellegrino	1	-0/+0

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	R worksheet to explore the data from the HDF5 file.	Don Pellegrino	1	-0/+19

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

2010-01-16	Annotated the inimplemented methods of aggregator. This serves as a todo lis...	Don Pellegrino	1	-0/+0

2010-01-16	Added thoughts on the value provided by the HDF5 container.	Don Pellegrino	1	-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.
2010-01-16	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	Added compilation output to the ignore list.	Don Pellegrino	1	-0/+4

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.
2010-01-15	Added output of GNU Autotools to the ignore list.	Don Pellegrino	1	-0/+15

2010-01-15	Added files for initialization and use of the GNU Autotools.	Don Pellegrino	6	-0/+33

2010-01-15	Initial check-in.	Don Pellegrino	3	-0/+310