Package Bio :: Package SeqIO :: Module TabIO
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Module TabIO

source code

Bio.SeqIO support for the "tab" (simple tab separated) file format.

You are expected to use this module via the Bio.SeqIO functions.

The "tab" format is an ad-hoc plain text file format where each sequence is
on one (long) line.  Each line contains the identifier/description, followed
by a tab, followed by the sequence.  For example, consider the following
short FASTA format file:

>ID123456 possible binding site?
CATCNAGATGACACTACGACTACGACTCAGACTAC
>ID123457 random sequence
ACACTACGACTACGACTCAGACTACAAN

Apart from the descriptions, this can be represented in the simple two column
tab separated format as follows:

ID123456(tab)CATCNAGATGACACTACGACTACGACTCAGACTAC
ID123457(tab)ACACTACGACTACGACTCAGACTACAAN

When reading this file, "ID123456" or "ID123457" will be taken as the record's
.id and .name property.  There is no other information to record.

Similarly, when writing to this format, Biopython will ONLY record the record's
.id and .seq (and not the description or any other information) as in the
example above.

Classes [hide private]
  TabWriter
Class to write simple tab separated format files.
Functions [hide private]
 
TabIterator(handle, alphabet=SingleLetterAlphabet())
Iterates over tab separated lines (as SeqRecord objects).
source code
Variables [hide private]
  __package__ = 'Bio.SeqIO'
Function Details [hide private]

TabIterator(handle, alphabet=SingleLetterAlphabet())

source code 
Iterates over tab separated lines (as SeqRecord objects).

Each line of the file should contain one tab only, dividing the line
into an identifier and the full sequence.

handle - input file
alphabet - optional alphabet

The first field is taken as the record's .id and .name (regardless of
any spaces within the text) and the second field is the sequence.

Any blank lines are ignored.