Blast Stylesheet
2
I'd like to create an HTML file (from the XML file and XSL stylesheet) similar to what It can be achieved when we performed a BLAST search on the NCBI server. What is the use of this file (xml) is the most appropriate or should i use another kind of out of blast (ASN. ...), and are there any examples of such a XSL file to format .
blast
xml
format
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updated 2.9 years ago by
Ram
44k
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written 13.7 years ago by
Yann
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70
Update : I wrote the XSLT stylesheet. It is available on github .
Example :
The XML:
(..)
<Hit>
<Hit_num>2</Hit_num>
<Hit_id>gi|27881483|ref|NM_017590.4|</Hit_id>
<Hit_def>Homo sapiens zinc finger CCCH-type containing 7B (ZC3H7B), mRNA</Hit_def>
<Hit_accession>NM_017590</Hit_accession>
<Hit_len>5868</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>114.899</Hsp_bit-score>
<Hsp_score>126</Hsp_score>
<Hsp_evalue>1.2149e-23</Hsp_evalue>
<Hsp_query-from>896</Hsp_query-from>
<Hsp_query-to>1302</Hsp_query-to>
<Hsp_hit-from>2927</Hsp_hit-from>
<Hsp_hit-to>2518</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>-1</Hsp_hit-frame>
<Hsp_identity>280</Hsp_identity>
<Hsp_positive>280</Hsp_positive>
<Hsp_gaps>17</Hsp_gaps>
<Hsp_align-len>417</Hsp_align-len>
<Hsp_qseq>CCTTCTGGGCAGG---TGCCATTCATATACCTATCACAAATACTGAAATAGCCTGTTGGGAAGCGGTGCTGCCAGCAGTACTGGTCGTCC---TCGGTGTGGAAAAC
CTTCTCTTTGTGCTTCTCGGAGGAGATGTGGCCCTGCCACTGCTTCTCACTGTTGCAGTTTTTCCCACACATCCAGCAGTGAAAGTCCACTGTAACTTCAGCATAATCTGTTGGCATGTGAAT
TTG-TTTTCCATTTTCCTTGTTTGACTGACTGGCTAT---GTCTTCACTTTTTTCATTTTTTTGACTCTTGAGCCATAGTTCGTAAAATTGCTCCATATCTTGTATCCCATTCTCCTTCATGT
AAGTCCAAACTTCTCTTTCCTCAGGACTATGAGCAAAGGAACAGTTTCCAACATATTGACATTT</Hsp_qseq>
<Hsp_hseq>CCATCTGGGCAGGCTTTGCCCTTCTGGAGCCTGTCGCAGAGCCGGAACTCGCCCATGGGGAAGCGGAAGGCCCAGCCG--CTGG-CGTCACTGTCGGACGTGAAGAC
CTTCTCCTTGTGCTTCTCGGACTGGATGTGCTGCTGCCACTGCTTCTTGCTGTTGCTGTTCTTGCCGCAGAGCCAGCAGTGGTAGCCCATCATGATGTCCGCGTAGTCCGTGGGCATCTGGAT
CTGCTTCTCCCCTTCCCGAG---AACTGA-TGGGGGTCCCTTCTCCAGGCTTTCCTGGGTTGTGTTTTTTCAGCCACATGTCATAGGTCTGCTGCATGTCCAGGATCTTGTTCTCCTTCATGA
AGGTCCACATGTCCCTCTCCTCCGGGCTGTGTGCGAAGGAGCAGTTCCCCACATATTGGCACTT</Hsp_hseq>
<Hsp_midline>|| |||||||||| |||| ||| ||| || || | | ||| | ||| | ||||||||| ||||| | |||| |||| |||| |||
|||||||| |||||||||||||| |||||| |||||||||||||| ||||||| ||| || || || | ||||||||| || ||| | | || || || || || ||||| ||
|| || || ||| || || | ||||| ||| | ||| || ||| | || || | || ||||| | || || |||| ||| || | ||| ||||||||||
|| | ||||| | || || ||||| || || || || ||||| ||||| || |||||||| || ||</Hsp_midline>
</Hsp>
</Hit_hsps>
(...)
Run the stylesheet:
xsltproc --novalid blast2html.xsl blast.xml
Result :
(...)
>gi|27881483|ref|NM_017590.4||NM_017590|Homo sapiens zinc finger CCCH-type containing 7B (ZC3H7B), mRNA
Length=5868
Score = 114.899 bits (126), Expect = 1.2149e-23
Identities = 280/417 (67.1462829736211%), Gaps = 17/417 (4.07673860911271%)
Strand = Plus/Minus
Query 896 CCTTCTGGGCAGG---TGCCATTCATATACCTATCACAAATACTGAAATAGCCTGTTGGG 952
|| |||||||||| |||| ||| ||| || || | | ||| | ||| | |||
Sbjct 2927 CCATCTGGGCAGGCTTTGCCCTTCTGGAGCCTGTCGCAGAGCCGGAACTCGCCCATGGGG 2868
Query 953 AAGCGGTGCTGCCAGCAGTACTGGTCGTCC---TCGGTGTGGAAAACCTTCTCTTTGTGC 1009
|||||| ||||| | |||| |||| |||| ||| |||||||| ||||||
Sbjct 2867 AAGCGGAAGGCCCAGCCG--CTGG-CGTCACTGTCGGACGTGAAGACCTTCTCCTTGTGC 2811
Query 1010 TTCTCGGAGGAGATGTGGCCCTGCCACTGCTTCTCACTGTTGCAGTTTTTCCCACACATC 1069
|||||||| |||||| |||||||||||||| ||||||| ||| || || || | |
Sbjct 2810 TTCTCGGACTGGATGTGCTGCTGCCACTGCTTCTTGCTGTTGCTGTTCTTGCCGCAGAGC 2751
Query 1070 CAGCAGTGAAAGTCCACTGTAACTTCAGCATAATCTGTTGGCATGTGAATTTG-TTTTCC 1128
|||||||| || ||| | | || || || || || ||||| || || || || |||
Sbjct 2750 CAGCAGTGGTAGCCCATCATGATGTCCGCGTAGTCCGTGGGCATCTGGATCTGCTTCTCC 2691
Query 1129 ATTTTCCTTGTTTGACTGACTGGCTAT---GTCTTCACTTTTTTCATTTTTTTGACTCTT 1185
|| || | ||||| ||| | ||| || ||| | || || | ||
Sbjct 2690 CCTTCCCGAG---AACTGA-TGGGGGTCCCTTCTCCAGGCTTTCCTGGGTTGTGTTTTTT 2635
Query 1186 GAGCCATAGTTCGTAAAATTGCTCCATATCTTGTATCCCATTCTCCTTCATGTAAGTCCA 1245
||||| | || || |||| ||| || | ||| |||||||||||| | |||||
Sbjct 2634 CAGCCACATGTCATAGGTCTGCTGCATGTCCAGGATCTTGTTCTCCTTCATGAAGGTCCA 2575
Query 1246 AACTTCTCTTTCCTCAGGACTATGAGCAAAGGAACAGTTTCCAACATATTGACATTT 1302
| || || ||||| || || || || ||||| ||||| || |||||||| || ||
Sbjct 2574 CATGTCCCTCTCCTCCGGGCTGTGTGCGAAGGAGCAGTTCCCCACATATTGGCACTT 2518
(...)
I wrote a stylesheet to display the blast output as SVG+XHTML. Transforming to XHTML should be even easier.
See my post .
or a quick search in google returned this page
Hi all,
I implemented some time ago several Java XML wrapper classes for dealing with XML output from Blast.
They are available in this GitHub repository , (this project also includes many other general bioinformatics related XML wrappers) .
These are some of the elements modelled:
Hope this can be useful.
Cheers,
Pablo
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why did I get a downvote ? :-)
Many thanks Pierre
Hi Pierre,
This looks like an excellent xsl ... does it still work? I tried running the command you detailed against a blastn xml and it is returning many errors.
Many thanks,
Sean
For example (below). Any pointers would be much appreciated.
Thanks very much, Sean
OK I found a newer version in your Github repo: https://github.com/lindenb/xslt-sandbox
It works a with some issues on Firefox ... Chrome just renders text.
Thanks you.