Package SeqIO
source code
Sequence input/output as SeqRecord objects.
The Bio.SeqIO module is also documented by a whole chapter in the Biopython
tutorial, and by the wiki http://biopython.org/wiki/SeqIO on the website.
The approach is designed to be similar to the bioperl SeqIO design.
Input
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The main function is Bio.SeqIO.parse(...) which takes an input file handle,
and format string. This returns an iterator giving SeqRecord objects.
from Bio import SeqIO
handle = open("example.fasta", "rU")
for record in SeqIO.parse(handle, "fasta") :
print record
handle.close()
Note that the parse() function will all invoke the relevant parser for the
format with its default settings. You may want more control, in which case
you need to create a format specific sequence iterator directly.
For non-interlaced files (e.g. Fasta, GenBank, EMBL) with multiple records
using a sequence iterator can save you a lot of memory (RAM). There is
less benefit for interlaced file formats (e.g. most multiple alignment file
formats). However, an iterator only lets you access the records one by one.
If you want random access to the records by number, turn this into a list:
from Bio import SeqIO
handle = open("example.fasta", "rU")
records = list(SeqIO.parse(handle, "fasta"))
handle.close()
print records[0]
If you want random access to the records by a key such as the record id,
turn the iterator into a dictionary:
from Bio import SeqIO
handle = open("example.fasta", "rU")
record_dict = SeqIO.to_dict(SeqIO.parse(handle, "fasta"))
handle.close()
print record["gi:12345678"]
If you expect your file to contain one-and-only-one record, then we provide
the following 'helper' function which will return a single SeqRecord, or
raise an exception if there are no records or more than one record:
from Bio import SeqIO
handle = open("example.fasta", "rU")
record = SeqIO.read(handle, "fasta")
handle.close()
print record
This style is useful when you expect a single record only (and would
consider multiple records an error). For example, when dealing with GenBank
files for bacterial genomes or chromosomes, there is normally only a single
record. Alternatively, use this with a handle when download a single record
from the internet.
However, if you just want the first record from a file containing multiple
record, use the iterator's next() method:
from Bio import SeqIO
handle = open("example.fasta", "rU")
record = SeqIO.parse(handle, "fasta").next()
handle.close()
print record
The above code will work as long as the file contains at least one record.
Note that if there is more than one record, the remaining records will be
silently ignored.
Input - Alignments
==================
You can read in alignment files as Alignment objects using Bio.AlignIO.
Alternatively, reading in an alignment file format via Bio.SeqIO will give
you a SeqRecord for each row of each alignment.
Output
======
Use the function Bio.SeqIO.write(...), which takes a complete set of
SeqRecord objects (either as a list, or an iterator), an output file handle
and of course the file format.
from Bio import SeqIO
records = ...
handle = open("example.faa", "w")
SeqIO.write(records, handle, "fasta")
handle.close()
In general, you are expected to call this function once (with all your
records) and then close the file handle.
Output - Advanced
=================
The effect of calling write() multiple times on a single file will vary
depending on the file format, and is best avoided unless you have a strong
reason to do so.
Trying this for certain alignment formats (e.g. phylip, clustal, stockholm)
would have the effect of concatenating several multiple sequence alignments
together. Such files are created by the PHYLIP suite of programs for
bootstrap analysis.
For sequential files formats (e.g. fasta, genbank) each "record block" holds
a single sequence. For these files it would probably be safe to call
write() multiple times.
File Formats
============
When specifying the file format, use lowercase strings. The same format
names are also used in Bio.AlignIO and include the following:
ace - Reads the contig sequences from an ACE assembly file.
embl - The EMBL flat file format. Uses Bio.GenBank internally.
fasta - The generic sequence file format where each record starts with
an identifer line starting with a ">" character, followed by
lines of sequence.
genbank - The GenBank or GenPept flat file format.
ig - The IntelliGenetics file format, apparently the same as the
MASE alignment format.
phd - Output from PHRED, used by PHRAP and CONSED for input.
pir - A "FASTA like" format introduced by the National Biomedical
Research Foundation (NBRF) for the Protein Information Resource
(PIR) database, now part of UniProt.
swiss - Plain text Swiss-Prot aka UniProt format.
tab - Simple two column tab separated sequence files, where each
line holds a record's identifier and sequence. For example,
this is used as by Aligent's eArray software when saving
microarray probes in a minimal tab delimited text file.
Note that while Bio.SeqIO can read all the above file formats, it cannot write
to all of them.
You can also use any file format supported by Bio.AlignIO, such as "nexus",
"phlip" and "stockholm", which gives you access to the individual sequences
making up each alignment as SeqRecords.
Further Information
===================
See the wiki page http://biopython.org/wiki/SeqIO and also the Bio.SeqIO
chapter in the Biopython Tutorial and Cookbook which is also available online:
http://biopython.org/DIST/docs/tutorial/Tutorial.html
http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
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write(sequences,
handle,
format)
Write complete set of sequences to a file. |
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parse(handle,
format,
alphabet=None)
Turns a sequence file into an iterator returning SeqRecords. |
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_iterate_via_AlignIO(handle,
format,
alphabet)
Iterate over all records in several alignments (PRIVATE). |
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_force_alphabet(record_iterator,
alphabet)
Iterate over records, over-riding the alphabet (PRIVATE). |
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read(handle,
format,
alphabet=None)
Turns a sequence file into a single SeqRecord. |
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to_dict(sequences,
key_function=None)
Turns a sequence iterator or list into a dictionary. |
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Write complete set of sequences to a file.
sequences - A list (or iterator) of SeqRecord objects. handle -
File handle object to write to. format - lower case string describing
the file format to write.
You should close the handle after calling this function.
Returns the number of records written (as an integer).
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Turns a sequence file into an iterator returning SeqRecords.
handle - handle to the file.
format - lower case string describing the file format.
alphabet - optional Alphabet object, useful when the sequence type cannot
be automatically inferred from the file itself (e.g. fasta)
Typical usage, opening a file to read in, and looping over the record(s):
>>> from Bio import SeqIO
>>> filename = "Nucleic/sweetpea.nu"
>>> for record in SeqIO.parse(open(filename,"rU"), "fasta") :
... print "ID", record.id
... print "Sequence length", len(record)
... print "Sequence alphabet", record.seq.alphabet
ID gi|3176602|gb|U78617.1|LOU78617
Sequence length 309
Sequence alphabet SingleLetterAlphabet()
For file formats like FASTA where the alphabet cannot be determined, it
may be useful to specify the alphabet explicitly:
>>> from Bio import SeqIO
>>> from Bio.Alphabet import generic_dna
>>> filename = "Nucleic/sweetpea.nu"
>>> for record in SeqIO.parse(open(filename,"rU"), "fasta", generic_dna) :
... print "ID", record.id
... print "Sequence length", len(record)
... print "Sequence alphabet", record.seq.alphabet
ID gi|3176602|gb|U78617.1|LOU78617
Sequence length 309
Sequence alphabet DNAAlphabet()
If you have a string 'data' containing the file contents, you must
first turn this into a handle in order to parse it:
from Bio import SeqIO
from StringIO import StringIO
my_iterator = SeqIO.parse(StringIO(data), format)
Use the Bio.SeqIO.read(handle, format) function when you expect a single
record only.
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Turns a sequence file into a single SeqRecord.
handle - handle to the file.
format - string describing the file format.
alphabet - optional Alphabet object, useful when the sequence type cannot
be automatically inferred from the file itself (e.g. fasta)
This function is for use parsing sequence files containing
exactly one record. For example, reading a GenBank file:
>>> from Bio import SeqIO
>>> record = SeqIO.read(open("GenBank/arab1.gb", "rU"), "genbank")
>>> print "ID", record.id
ID AC007323.5
>>> print "Sequence length", len(record)
Sequence length 86436
>>> print "Sequence alphabet", record.seq.alphabet
Sequence alphabet IUPACAmbiguousDNA()
If the handle contains no records, or more than one record,
an exception is raised. For example:
>>> from Bio import SeqIO
>>> record = SeqIO.read(open("GenBank/cor6_6.gb", "rU"), "genbank")
Traceback (most recent call last):
...
ValueError: More than one record found in handle
If however you want the first record from a file containing
multiple records this function would raise an exception (as
shown in the example above). Instead use:
>>> from Bio import SeqIO
>>> record = SeqIO.parse(open("GenBank/cor6_6.gb", "rU"), "genbank").next()
>>> print "First record's ID", record.id
First record's ID X55053.1
Use the Bio.SeqIO.parse(handle, format) function if you want
to read multiple records from the handle.
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Turns a sequence iterator or list into a dictionary.
sequences - An iterator that returns SeqRecord objects,
or simply a list of SeqRecord objects.
key_function - Optional function which when given a SeqRecord
returns a unique string for the dictionary key.
e.g. key_function = lambda rec : rec.name
or, key_function = lambda rec : rec.description.split()[0]
If key_function is ommitted then record.id is used, on the
assumption that the records objects returned are SeqRecords
with a unique id field.
If there are duplicate keys, an error is raised.
Example usage, defaulting to using the record.id as key:
>>> from Bio import SeqIO
>>> handle = open("GenBank/cor6_6.gb", "rU")
>>> format = "genbank"
>>> id_dict = SeqIO.to_dict(SeqIO.parse(handle, format))
>>> print id_dict.keys()
['L31939.1', 'AJ237582.1', 'X62281.1', 'AF297471.1', 'X55053.1', 'M81224.1']
>>> print id_dict["L31939.1"].description
Brassica rapa (clone bif72) kin mRNA, complete cds.
A more complex example, using the key_function argument in order to use
a sequence checksum as the dictionary key:
>>> from Bio import SeqIO
>>> from Bio.SeqUtils.CheckSum import seguid
>>> handle = open("GenBank/cor6_6.gb", "rU")
>>> format = "genbank"
>>> seguid_dict = SeqIO.to_dict(SeqIO.parse(handle, format), key_function = lambda rec : seguid(rec.seq))
>>> for key, record in seguid_dict.iteritems() :
... print key, record.id
SabZaA4V2eLE9/2Fm5FnyYy07J4 X55053.1
l7gjJFE6W/S1jJn5+1ASrUKW/FA X62281.1
/wQvmrl87QWcm9llO4/efg23Vgg AJ237582.1
TtWsXo45S3ZclIBy4X/WJc39+CY M81224.1
uVEYeAQSV5EDQOnFoeMmVea+Oow AF297471.1
BUg6YxXSKWEcFFH0L08JzaLGhQs L31939.1
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to_alignment(sequences,
alphabet=None,
strict=True)
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Returns a multiple sequence alignment (OBSOLETE).
sequences -An iterator that returns SeqRecord objects,
or simply a list of SeqRecord objects.
All the record sequences must be the same length.
alphabet - Optional alphabet. Stongly recommended.
strict - Optional, defaults to True. Should error checking
be done?
Using this function is now discouraged. Rather doing this:
from Bio import SeqIO
alignment = SeqIO.to_alignment(SeqIO.parse(handle, format))
You are now encouraged to use Bio.AlignIO instead, e.g.
from Bio import AlignIO
alignment = AlignIO.read(handle, format)
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Run the Bio.SeqIO module's doctests.
This will try and locate the unit tests directory, and run the
doctests from there in order that the relative paths used in the examples
work.
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_FormatToIterator
- Value:
{"fasta": FastaIO.FastaIterator, "genbank": InsdcIO.GenBankIterator, "
genbank-cds": InsdcIO.GenBankCdsFeatureIterator, "embl": InsdcIO.EmblI
terator, "embl-cds": InsdcIO.EmblCdsFeatureIterator, "ig": IgIO.IgIter
ator, "swiss": SwissIO.SwissIterator, "phd": PhdIO.PhdIterator, "ace":
AceIO.AceIterator, "tab": TabIO.TabIterator, "pir": PirIO.PirIterator
,}
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_FormatToWriter
- Value:
{"fasta": FastaIO.FastaWriter, "genbank": InsdcIO.GenBankWriter, "tab"
: TabIO.TabWriter,}
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