Is there any tool/scripts that are already out there that can parse standard blast.txt output? I can provide an example of my output if that would help?
I am learning bioinformatics and recently run my first major scripts which used blastn and received standard blast.txt output. I need a tool to parse the output to report the following:
I am familiar with python somewhat and feel that would be my best tool to work on first. I thank you in advance for your assistance and kindly time you spent reading this question.
If you're familiar with python then use the Biopython. Easily you can parse all the information you want form the standard output of blast.
Yes, tabular output (format 6) will give you 1 and 2. For taxonomy, I would recommend adding this field to the default blast output
-outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids"
Which can then be used to get the full lineage information form the taxonomy database (you can also do it with GI IDs, but this is more straight forward.
Interesting. When I read the blastn --help documentation, for example, I thought it would be -m 6. In reality, it is -outfmt "6 whatever field values I need"? I assume this is the same for blastx? If so, can you please provide me the documentation source where qseqid, sseqid, pident, and so on are documented and described? I would like to learn more please.
Most importantly, many humble thanks for your helpful response.
Yes, just type blastn -help and you will find the documentation for these options. The complete list is as follows:
Options 6, 7, and 10 can be additionally configured to produce
a custom format specified by space delimited format specifiers.
The supported format specifiers are:
qseqid means Query Seq-id
qgi means Query GI
qacc means Query accesion
qaccver means Query accesion.version
qlen means Query sequence length
sseqid means Subject Seq-id
sallseqid means All subject Seq-id(s), separated by a ';'
sgi means Subject GI
sallgi means All subject GIs
sacc means Subject accession
saccver means Subject accession.version
sallacc means All subject accessions
slen means Subject sequence length
qstart means Start of alignment in query
qend means End of alignment in query
sstart means Start of alignment in subject
send means End of alignment in subject
qseq means Aligned part of query sequence
sseq means Aligned part of subject sequence
evalue means Expect value
bitscore means Bit score
score means Raw score
length means Alignment length
pident means Percentage of identical matches
nident means Number of identical matches
mismatch means Number of mismatches
positive means Number of positive-scoring matches
gapopen means Number of gap openings
gaps means Total number of gaps
ppos means Percentage of positive-scoring matches
frames means Query and subject frames separated by a '/'
qframe means Query frame
sframe means Subject frame
btop means Blast traceback operations (BTOP)
staxids means unique Subject Taxonomy ID(s), separated by a ';'
(in numerical order)
sscinames means unique Subject Scientific Name(s), separated by a ';'
scomnames means unique Subject Common Name(s), separated by a ';'
sblastnames means unique Subject Blast Name(s), separated by a ';'
(in alphabetical order)
sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
(in alphabetical order)
stitle means Subject Title
salltitles means All Subject Title(s), separated by a '<>'
sstrand means Subject Strand
qcovs means Query Coverage Per Subject
qcovhsp means Query Coverage Per HSP
When not provided, the default value is:
'qseqid sseqid pident length mismatch gapopen qstart qend sstart send
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I am thinking about rerunning this and producing tabular output. If I did, would there be a tool to easily do the same thing as I wrote above?
Tabular output is much easier to parse than the text format or some of the other formats. You can also more easily customize the output in tabular formats.
Can Biopython easily parse this format as well?
Not sure about BioPython, but parsing tab delimited files in python is very easy.