Dear all, I'm new to pytables. I would use this package to store biological data. In practice I have 2 input files. The first consists in a long string of characters. The length is in the range 10e7-10e8. I have to read such file character by character and store it in a table according to its position (counting from 1). For example:
1 A 2 C 3 G 4 T and so on. Then, I have to read a second file and during the reading I have to associate to each character of the previous table another character, according to the position. Example: 1 A A 2 C C 3 G G 4 T T and so on. However, the same position can occur a variable number of times and so I have to associate a variable number of characters to each position. Example: 1 A AAAAA 2 C CCCCTC 3 G GGGGAGGGG 4 T TGGGTGTTTTTTTT and so on. I tried to use a vlarray for each position, updating the array every time needed. However, I noted that the creation of table according to the first structure above was very fast. Adding the vlarray I noted, instead, a drammatic performance reductiion in term of time (from seconds to many hours [I stopped the script before the conclution]). Is there a way to speed up the process when there are vlarray? I also tried to use the same table with a very long string size instead of vlarray but also in this case the time needed to buil the table was very high. Since I don't known very well pytables, is there a way to improve the performance? Thank you very much in advance for any help. Ernesto ------------------------------------------------------------------------------ Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev _______________________________________________ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
