BLAST+6 format (skbio.io.format.blast6)#
The BLAST+6 format (blast+6) stores the results of a BLAST [1] database
search. The results are stored in a simple tabular format with no column
headers. Values are separated by the tab character.
An example BLAST+6-formatted file comparing two protein sequences, taken
from [2] (tab characters represented by <tab>):
moaC<tab>gi|15800534|ref|NP_286546.1|<tab>100.00<tab>161<tab>0<tab>0
<tab>1<tab>161<tab>1<tab>161<tab>3e-114<tab>330
moaC<tab>gi|170768970|ref|ZP_02903423.1|<tab>99.38<tab>161<tab>1<tab>0
<tab>1<tab>161<tab>1<tab>161<tab>9e-114<tab>329
Format Support#
Has Sniffer: No
Reader |
Writer |
Object Class |
|---|---|---|
Yes |
No |
|
Format Specification#
BLAST+6 format is a tabular text-based format produced by both BLAST+ output
format 6 (-outfmt 6) and legacy BLAST output format 8 (-m 8). It is
tab-separated and has no column headers. With BLAST+, users can specify the
columns that are present in their BLAST output file by specifying column names
(e.g., -outfmt "6 qseqid sseqid bitscore qstart sstart"), if the default
columns output by BLAST are not desired.
BLAST Column Types#
The following column types are output by BLAST and supported by scikit-bio. This information is taken from [3].
Name |
Description |
Type |
|---|---|---|
qseqid |
Query Seq-id |
str |
qgi |
Query GI |
int |
qacc |
Query accesion |
str |
qaccver |
Query accesion.version |
str |
qlen |
Query sequence length |
int |
sseqid |
Subject Seq-id |
str |
sallseqid |
All subject Seq-id(s), separated by a ‘;’ |
str |
sgi |
Subject GI |
int |
sallgi |
All subject GIs |
int |
sacc |
Subject accesion |
str |
saccver |
Subject accesion.version |
str |
sallacc |
All subject accesions |
str |
slen |
Subject sequence length |
int |
qstart |
Start of alignment in query |
int |
qend |
End of alignment in query |
int |
sstart |
Start of alignment in subject |
int |
send |
End of alignment in subject |
int |
qseq |
Aligned part of query sequence |
str |
sseq |
Aligned part of subject sequence |
str |
evalue |
Expect value |
float |
bitscore |
Bit score |
float |
score |
Raw score |
int |
length |
Alignment length |
int |
pident |
Percent of identical matches |
float |
nident |
Number of identical matches |
int |
mismatch |
Number of mismatches |
int |
positive |
Number of positive-scoring matches |
int |
gapopen |
Number of gap openings |
int |
gaps |
Total number of gaps |
int |
ppos |
Percentage of positive-scoring matches |
float |
frames |
Query and subject frames separated by a ‘/’ |
str |
qframe |
Query frame |
int |
sframe |
Subject frame |
int |
btop |
Blast traceback operations (BTOP) |
int |
staxids |
Unique Subject Taxonomy ID(s), separated by a ‘;’ (in numerical order). |
str |
sscinames |
Unique Subject Scientific Name(s), separated by a ‘;’ |
str |
scomnames |
Unique Subject Common Name(s), separated by a ‘;’ |
str |
sblastnames |
unique Subject Blast Name(s), separated by a ‘;’ (in alphabetical order) |
str |
sskingdoms |
unique Subject Super Kingdom(s), separated by a ‘;’ (in alphabetical order) |
str |
stitle |
Subject Title |
str |
sstrand |
Subject Strand |
str |
salltitles |
All Subject Title(s), separated by a ‘<>’ |
str |
qcovs |
Query Coverage Per Subject |
int |
qcovhsp |
Query Coverage Per HSP |
int |
Note
When a BLAST+6-formatted file contains N/A values, scikit-bio
will convert these values into np.nan, matching pandas’ convention for
representing missing data.
Note
scikit-bio stores columns of type int as type float in the
returned pd.DataFrame. This is necessary in order to allow N/A
values in integer columns (this is currently a limitation of pandas).
Format Parameters#
The following format parameters are available in blast+6 format:
default_columns:Falseby default. IfTrue, will use the default columns output by BLAST, which are qseqid, sseqid, pident, length, mismatch, gapopen, qstart, qend, sstart, send, evalue, and bitscore.Warning
When reading legacy BLAST files, you must pass
default_columns=Truebecause legacy BLAST does not allow users to specify which columns are present in the output file.columns:Noneby default. If provided, must be a list of column names in the order they will appear in the file.
Note
Either default_columns or columns must be provided, as
blast+6 does not contain column headers.
Examples#
Suppose we have a blast+6 file with default columns:
>>> from io import StringIO
>>> import skbio.io
>>> import pandas as pd
>>> fs = '\n'.join([
... 'moaC\tgi|15800534|ref|NP_286546.1|\t100.00\t161\t0\t0\t1\t161\t1\t161'
... '\t3e-114\t330',
... 'moaC\tgi|170768970|ref|ZP_02903423.1|\t99.38\t161\t1\t0\t1\t161\t1'
... '\t161\t9e-114\t329'
... ])
>>> fh = StringIO(fs)
Read the file into a pd.DataFrame and specify that default columns should
be used:
>>> df = skbio.io.read(fh, format="blast+6", into=pd.DataFrame,
... default_columns=True)
>>> df
qseqid sseqid pident length mismatch gapopen \
0 moaC gi|15800534|ref|NP_286546.1| 100.00 161.0 0.0 0.0
1 moaC gi|170768970|ref|ZP_02903423.1| 99.38 161.0 1.0 0.0
qstart qend sstart send evalue bitscore
0 1.0 161.0 1.0 161.0 3.000000e-114 330.0
1 1.0 161.0 1.0 161.0 9.000000e-114 329.0
Suppose we have a blast+6 file with user-supplied (non-default) columns:
>>> from io import StringIO
>>> import skbio.io
>>> import pandas as pd
>>> fs = '\n'.join([
... 'moaC\t100.00\t0\t161\t0\t161\t330\t1',
... 'moaC\t99.38\t1\t161\t0\t161\t329\t1'
... ])
>>> fh = StringIO(fs)
Read the file into a pd.DataFrame and specify which columns are present
in the file:
>>> df = skbio.io.read(fh, format="blast+6", into=pd.DataFrame,
... columns=['qseqid', 'pident', 'mismatch', 'length',
... 'gapopen', 'qend', 'bitscore', 'sstart'])
>>> df
qseqid pident mismatch length gapopen qend bitscore sstart
0 moaC 100.00 0.0 161.0 0.0 161.0 330.0 1.0
1 moaC 99.38 1.0 161.0 0.0 161.0 329.0 1.0
References#
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) “Basic local alignment search tool.” J. Mol. Biol. 215:403-410.