biopython

v1.71.0

biopython v1.71.0 Bio.SeqIO.TabIO

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.

Link to this section Summary

Functions

TabIterator()

Iterates over tab separated lines (as SeqRecord objects)

Link to this section Functions

Link to this function TabIterator()

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.

Arguments:

  • 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.

Example:

 >>> with open("GenBank/NC_005816.tsv") as handle:
 ...     for record in TabIterator(handle):
 ...         print("%s length %i" % (record.id, len(record)))
 gi|45478712|ref|NP_995567.1| length 340
 gi|45478713|ref|NP_995568.1| length 260
 gi|45478714|ref|NP_995569.1| length 64
 gi|45478715|ref|NP_995570.1| length 123
 gi|45478716|ref|NP_995571.1| length 145
 gi|45478717|ref|NP_995572.1| length 357
 gi|45478718|ref|NP_995573.1| length 138
 gi|45478719|ref|NP_995574.1| length 312
 gi|45478720|ref|NP_995575.1| length 99
 gi|45478721|ref|NP_995576.1| length 90