Python Tools for Computational Molecular Biology
Python Tools for Computational Molecular Biology
This page describes Bio.AlignIO, a new multiple sequence Alignment
Input/Output interface for BioPython 1.46 and later.
In addition to the built in API documentation, there is a whole chapter
in the Tutorial
on Bio.AlignIO, and although there is some overlap it is well worth
reading in addition to this page. There is also the API
documentation
(which you can read online, or from within Python with the help()
command).
You may already be familiar with the Bio.SeqIO
module which deals with files containing one or more sequences
represented as SeqRecord objects. The purpose of
the SeqIO module is to provide a simple uniform interface to assorted
sequence file formats.
Similarly, Bio.AlignIO deals with files containing one or more sequence
alignments represented as Alignment objects. Bio.AlignIO uses the same
set of functions for input and output as in Bio.SeqIO, and the same
names for the file formats supported.
Note that the inclusion of Bio.AlignIO does lead to some duplication or
choice in how to deal with some file formats. For example, Bio.AlignIO
and Bio.Nexus will both read alignments from NEXUS files - but
Bio.NEXUS allows more control and the use of trees.
My vision is that for reading or writing sequence alignments you should
try Bio.AlignIO as your first choice. In some cases you may only care
about the sequences themselves, in which case try using
Bio.SeqIO on the alignment file directly. Unless you
have some very specific requirements, I hope this should suffice.
This table lists the file formats that Bio.AlignIO can read and write, with the Biopython version where this was first supported.
The format name is a simple lowercase string, matching the names used in Bio.SeqIO. Where possible we use the same name as BioPerl’s SeqIO and EMBOSS.
| Format name | Reads | Writes | Notes |
|---|---|---|---|
| clustal | 1.46 | 1.46 | The alignment format of Clustal X and Clustal W. |
| emboss | 1.46 | No | The EMBOSS simple/pairs alignment format. |
| fasta | 1.46 | 1.48 | This refers to the input file format introduced for Bill Pearson’s FASTA tool, where each record starts with a “>” line. Note that storing more than one alignment in this format is ambiguous. Writing FASTA files with AlignIO failed prior to release 1.48 (Bug 2557). |
| fasta-m10 | 1.46 | No | This refers to the pairwise alignment output from Bill Pearson’s FASTA tools, specifically the machine readable version when the -m 10 command line option is used. The default free format text output from the FASTA tools is not supported. |
| ig | 1.47 | No | The refers to the IntelliGenetics file format often used for ordinary un-aligned sequences. The tool MASE also appears to use the same file format for alignments, hence its inclusion in this table. See MASE format. |
| maf | 1.69 | 1.69 | Multiple Alignment Format (MAF) produced by Multiz. Used to store whole-genome alignments, such as the 30-way alignments available from the UCSC genome browser. |
| mauve | 1.70 | 1.70 | Mauve’s eXtended Multi-FastA (XMFA) file format |
| msf | 1.75 | No | GCG MSF file format. |
| nexus | 1.46 | 1.48 | Also known as PAUP format. Uses Bio.Nexus internally. Only one alignment per file is supported. |
| phylip | 1.46 | 1.46 | This is a strict interpretation of the interlaced PHYLIP format which truncates names at 10 characters. |
| phylip-sequential | 1.59 | 1.59 | This is a strict interpretation of the sequential PHYLIP format which truncates names at 10 characters. |
| phylip-relaxed | 1.58 | 1.58 | This is a relaxed interpretation of the PHYLIP format which allows long names. |
| stockholm | 1.46 | 1.46 | Also known as PFAM format, this file format supports rich annotation. |
In addition, you can store the (gapped) sequences from an alignment in many of the file formats supported by Bio.SeqIO. The most common example of this is storing alignments in the simple fasta format. However, storing more than one alignment in a single such file is ambiguous - and this is not recommended.
As in Bio.SeqIO, there are two functions for
alignment input. These are Bio.AlignIO.read() for when the file
contains one and only one alignment, and the more general
Bio.AlignIO.parse() when the file may contain multiple separate
alignments.
Both these functions have two required arguments, a file handle and a file format. As with Bio.SeqIO, Biopython insists that you explicitly give the expected file format, rather than attempting to guess this based on the filename or contents. The file format is specified as a lower case string, see the table above.
As an example, we’ll look at a PFAM seed alignment for the Fibrinogen gamma chain PF09395 Fib_gamma. At the time of writing, this contained 14 sequences with an alignment length of 77 amino acids, and is shown below in the PFAM or Stockholm format:
# STOCKHOLM 1.0
#=GS Q7ZVG7_BRARE/37-110 AC Q7ZVG7.1
#=GS Q6X871_SCAAQ/1-77 AC Q6X871.1
#=GS O02676_CROCR/1-77 AC O02676.1
#=GS Q6X869_TENEC/1-77 AC Q6X869.1
#=GS FIBG_HUMAN/40-116 AC P02679.3
#=GS O02689_TAPIN/1-77 AC O02689.1
#=GS O02688_PIG/1-77 AC O02688.1
#=GS O02672_9CETA/1-77 AC O02672.1
#=GS O02682_EQUPR/1-77 AC O02682.1
#=GS Q6X870_CYNVO/1-77 AC Q6X870.1
#=GS FIBG_RAT/40-116 AC P02680.3
#=GS Q6X866_DROAU/1-76 AC Q6X866.1
#=GS O93568_CHICK/40-116 AC O93568.1
#=GS FIBG_XENLA/38-114 AC P17634.1
Q7ZVG7_BRARE/37-110 GFGTYCPTTCGVADYLQRYKPDMDKKLDDMEQDLEEIANLTRGAQDKVVYLK---DSEAQAQKQSPDTYIKKSSNML
Q6X871_SCAAQ/1-77 RFGSYCPTTCGIADFLSTYQATVDKDLQTLEDILSQAENKTMEAKELVKAIQVSYLPEDPARPNRVELATKDSKKMM
O02676_CROCR/1-77 RFGSYCPTTCGIADFLSTYQTGVXNDLRTLEDLLSGIENKTSEAKELIKSIQVSYNPNEPPKPNTIVSATKDSKKMM
Q6X869_TENEC/1-77 RFGSYCPTTCGIADFLSTYQGSIDKDLQTLEDILNQVENKTXEASELIKSIQVSYNPDEPPRPNMIEGATQKSKKML
FIBG_HUMAN/40-116 RFGSYCPTTCGIADFLSTYQTKVDKDLQSLEDILHQVENKTSEVKQLIKAIQLTYNPDESSKPNMIDAATLKSRKML
#=GS FIBG_HUMAN/40-116 DR PDB; 1qvh L;14-45
#=GS FIBG_HUMAN/40-116 DR PDB; 1fza C;88-90
#=GS FIBG_HUMAN/40-116 DR PDB; 1fzb C;88-90
#=GS FIBG_HUMAN/40-116 DR PDB; 1fzb F;88-90
#=GS FIBG_HUMAN/40-116 DR PDB; 1qvh I;14-45
#=GS FIBG_HUMAN/40-116 DR PDB; 1fza F;88-90
#=GR FIBG_HUMAN/40-116 SS CCXCXBXXHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-CC
O02689_TAPIN/1-77 RFGSYCPTTCGIADFLSTYQTXVDKDLQVLEDILNQAENKTSEAKELIKAIQVRYKPDEPTKPGGIDSATRESKKML
O02688_PIG/1-77 RFGSYCPTMCGIAGFLSTYQNTVEKDLQNLEGILHQVENKTSEARELIKAIQISYNPEDLSKPDRIQSATKESKKML
O02672_9CETA/1-77 RFGSYCPTTCGVADFLSNYQTSVDKDLQNLEGILYQVENKTSEARELVKAIQISYNPDEPSKPNNIESATKNSKRMM
O02682_EQUPR/1-77 RFGSYCPTTCGIADFLSNYQTSVDKDLQDFEDILHRAENQTSEAEQLIQAIRTSYNPDEPPKTGRIDAATRESKKMM
Q6X870_CYNVO/1-77 RFGSYCPTTCGIADFLSTYQTKVDEDLQNLEDILYRVENRTSEAKELIKAIQVDYNPGEPPKQSVTEGATQNAKKMV
FIBG_RAT/40-116 RFGSYCPTTCGISDFLNSYQTDVDTDLQTLENILQRAENRTTEAKELIKAIQVYYNPDQPPKPGMIEGATQKSKKMV
Q6X866_DROAU/1-76 RFGSYCPTTCGIADFLNKYQTTIDQDLRHMEETLRDIDNKTAESTLLIQKIQIGQTPDPRPQ-NVIGDVTQKSRKMI
O93568_CHICK/40-116 RFGSYCPTTCGIADFFNKYRLTTDGELLEIEGLLQQATNSTGSIEYLIQHIKTIYPSEKQTLPQSIEQLTQKSKKII
#=GS O93568_CHICK/40-116 DR PDB; 1m1j F;14-90
#=GS O93568_CHICK/40-116 DR PDB; 1m1j C;14-90
#=GR O93568_CHICK/40-116 SS CCEEEEE-CCCCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHS-SSTT--SS-HHHHHHHHHHHH
FIBG_XENLA/38-114 RFGEYCPTTCGISDFLNRYQENVDTDLQYLENLLTQISNSTSGTTIIVEHLIDSGKKPATSPQTAIDPMTQKSKTCW
#=GC SS_cons CCECEEE-CCCCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHS-SSTT--SS-HHHHHHHHHHCC
#=GC seq_cons RFGSYCPTTCGIADFLSsYQssVDcDLQsLEsILpplEN+ToEAc-LIKuIQlsYsP--ss+PstI-uATpcSKKMl
//
You will notice that there is plenty of annotation information here, including accession numbers for each sequence and also some PDB database cross-references and secondary structure information for the human and chick fibrinogen proteins.
This file contains a single alignment, so we can use the
Bio.AlignIO.read() function to load it in Biopython. Let’s assume
you have downloaded this alignment from Sanger, or have copy and pasted
the text above, and saved this as a file called PF09395_seed.sth on
your computer. Then in python:
from Bio import AlignIO
alignment = AlignIO.read(open("PF09395_seed.sth"), "stockholm")
print("Alignment length %i" % alignment.get_alignment_length())
for record in alignment:
print(record.seq + " " + record.id)
That should give:
Alignment length 77
GFGTYCPTTCGVADYLQRYKPDMDKKLDDMEQDLEEIANLTRGAQDKVVYLK---DSEAQAQKQSPDTYIKKSSNML Q7ZVG7_BRARE/37-110
RFGSYCPTTCGIADFLSTYQATVDKDLQTLEDILSQAENKTMEAKELVKAIQVSYLPEDPARPNRVELATKDSKKMM Q6X871_SCAAQ/1-77
RFGSYCPTTCGIADFLSTYQTGVXNDLRTLEDLLSGIENKTSEAKELIKSIQVSYNPNEPPKPNTIVSATKDSKKMM O02676_CROCR/1-77
RFGSYCPTTCGIADFLSTYQGSIDKDLQTLEDILNQVENKTXEASELIKSIQVSYNPDEPPRPNMIEGATQKSKKML Q6X869_TENEC/1-77
RFGSYCPTTCGIADFLSTYQTKVDKDLQSLEDILHQVENKTSEVKQLIKAIQLTYNPDESSKPNMIDAATLKSRKML FIBG_HUMAN/40-116
RFGSYCPTTCGIADFLSTYQTXVDKDLQVLEDILNQAENKTSEAKELIKAIQVRYKPDEPTKPGGIDSATRESKKML O02689_TAPIN/1-77
RFGSYCPTMCGIAGFLSTYQNTVEKDLQNLEGILHQVENKTSEARELIKAIQISYNPEDLSKPDRIQSATKESKKML O02688_PIG/1-77
RFGSYCPTTCGVADFLSNYQTSVDKDLQNLEGILYQVENKTSEARELVKAIQISYNPDEPSKPNNIESATKNSKRMM O02672_9CETA/1-77
RFGSYCPTTCGIADFLSNYQTSVDKDLQDFEDILHRAENQTSEAEQLIQAIRTSYNPDEPPKTGRIDAATRESKKMM O02682_EQUPR/1-77
RFGSYCPTTCGIADFLSTYQTKVDEDLQNLEDILYRVENRTSEAKELIKAIQVDYNPGEPPKQSVTEGATQNAKKMV Q6X870_CYNVO/1-77
RFGSYCPTTCGISDFLNSYQTDVDTDLQTLENILQRAENRTTEAKELIKAIQVYYNPDQPPKPGMIEGATQKSKKMV FIBG_RAT/40-116
RFGSYCPTTCGIADFLNKYQTTIDQDLRHMEETLRDIDNKTAESTLLIQKIQIGQTPDPRPQ-NVIGDVTQKSRKMI Q6X866_DROAU/1-76
RFGSYCPTTCGIADFFNKYRLTTDGELLEIEGLLQQATNSTGSIEYLIQHIKTIYPSEKQTLPQSIEQLTQKSKKII O93568_CHICK/40-116
RFGEYCPTTCGISDFLNRYQENVDTDLQYLENLLTQISNSTSGTTIIVEHLIDSGKKPATSPQTAIDPMTQKSKTCW FIBG_XENLA/38-114
As in Bio.SeqIO, there is a single output function
Bio.AlignIO.write(). This takes three arguments: some alignments, a
file handle to write to, and the format to use.
As of Biopython 1.48, the alignment object acquired a .format()
method to give a string containing the alignment in the specified file
format, e.g.
AlignIO.read(open("PF09395_seed.sth"), "stockholm")
print(alignment.format("fasta"))
Please refer to the Bio.AlignIO chapter in the Tutorial for more details.
Suppose you have a file containing PHYLIP alignment(s) that you want to convert into the PFAM/Stockholm format:
from Bio import AlignIO
input_handle = open("example.phy", "rU")
output_handle = open("example.sth", "w")
alignments = AlignIO.parse(input_handle, "phylip")
AlignIO.write(alignments, output_handle, "stockholm")
output_handle.close()
input_handle.close()
By changing the format strings, that code could be used to convert between any supported file formats.