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Handbook of Normal Frames and Coordinates | Bozhidar Z. Iliev | Springer
For that r- son, the considerations and most of the proofs are given in details. Conventionally local coordinates or frames, which can be holonomic or not, are called normal if in them the coe? Until recently the ex- tence of normal frames was known proved only for symmetric linear connections on submanifolds of a manifold. Now the problems concerning normal frames for derivationsof thetensor algebraovera di? These rigorous results are important in conn- tion with some physical applications. It's nice to meet you. Details about Magnum freeRecommended present download handbook of normal frames to analyse a request learnt by Stanley Cavell.
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That means we can do this:. If you can get your sequences in a well annotated file format like GenBank or EMBL, then this sort of annotation information is much easier to deal with. In the previous section, we looked at parsing sequence data from a file. Instead of using a filename, you can give Bio. Here we use a file handle instead, using the with statement to close the handle automatically:. Now, suppose we have a gzip compressed file instead? These are very commonly used on Linux. In the previous sections, we looked at parsing sequence data from a file using a filename or handle , and from compressed files using a handle.
SeqIO with another type of handle, a network connection, to download and parse sequences from the internet. In general, you should probably download sequences once and save them to a file for reuse. Now remember, when you expect the handle to contain one and only one record, use the Bio. As a result, in Biopython 1. This time the handle contains multiple records, so we must use the Bio. As mentioned above, when you expect the handle to contain one and only one record, use the Bio. SeqIO module which allow dictionary like random access to a multi-sequence file. There is a trade off here between flexibility and memory usage.
In summary:. You can use the function Bio. There is just one required argument for Bio. Here we have just used the output from the SeqIO.
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As the name suggests, this returns a Python dictionary. We can access a single SeqRecord object via the keys and manipulate the object as normal:. However, typical dictionary construction methods will not deal with the case of repeated keys very nicely.
Using the Bio. Suppose you would rather have something else as the keys - like the accession numbers. This brings us nicely to SeqIO. First you must write your own function to return the key you want as a string when given a SeqRecord object. In general, the details of function will depend on the sort of input records you are dealing with. Then we can give this function to the SeqIO. This is a relatively recent checksum, and collisions should be very rare i. Now, recall the Bio. As the previous couple of examples tried to illustrate, using Bio. In general, this will only work on small to medium files.
For larger files you should consider Bio. Although it still returns a dictionary like object, this does not keep everything in memory. Instead, it just records where each record is within the file — when you ask for a particular record, it then parses it on demand. Note that Bio. There are good reasons for this, but it is a little technical. The second argument is the file format a lower case string as used in the other Bio.
SeqIO functions. Finally as an optional argument you can supply an alphabet, or a key function. Suppose you want to use the same keys as before? Much like with the Bio. Then we can give this function to the Bio. The dictionary-like object from Bio.
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However, it is sometimes useful to be able to get the original raw data straight from the file. A motivating example is extracting a subset of a records from a large file where either Bio. Also, you can index multiple files together providing all the record identifiers are unique. As of GenBank release , there are 38 files making up the viral sequences, gbvrl1. If you were interested in the viruses, you could download all the virus files from the command line very easily with the rsync command, and then decompress them with gunzip :.
Indexing the full set of virus GenBank files took about ten minutes on my machine, just the first four files took about a minute or so. However, once done, repeating this will reload the index file gbvrl. You can use the index as a read only Python dictionary - without having to worry about which file the sequence comes from, e. Just as with the Bio. Very often when you are indexing a sequence file it can be quite large — so you may want to compress it on disk.
Unfortunately efficient random access is difficult with the more common file formats like gzip and bzip2.