Blat Scripts: Difference between revisions
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Here is a collection of Blat-related Perl scripts | Here is a collection of Blat-related Perl scripts that perform functions that are frequently requested on the genome mailing list. If anyone finds a problem with these scripts then please notify me by selecting the e-mail user link from the side menu bar at: [[User:Hartera]] | ||
[[Media:BlatBot_pl.txt|BlatBot.pl]]: This is a script that takes a file of FASTA format sequences as input and then submits them to the web-based Blat on the UCSC Genome Browser web site. It obeys the site rules for the number of frequency of hits i.e. Program-driven use of the Genome Browser software is limited to a maximum of one hit every 15 seconds and | [[Media:BlatBot_pl.txt|BlatBot.pl]]: This is a script that takes a file of FASTA format sequences as input and then submits them to the web-based Blat on the UCSC Genome Browser web site. It obeys the site rules for the number of frequency of hits i.e. Program-driven use of the Genome Browser software is limited to a maximum of one hit every 15 seconds and Blats sequences in batches of 25 sequences at a time. | ||
The script usage is: | The script usage is: | ||
usage: BlatBot.pl <organism> <db> <searchType> <sortOrder> <input FASTA> <outputType> <output file> | usage: BlatBot.pl <organism> <db> <searchType> <sortOrder> <input FASTA> <outputType> <output file> | ||
Specify organism using the common name with first | Specify organism using the common name with first letter capitalized. | ||
e.g. Human, Mouse, Rat etc. | e.g. Human, Mouse, Rat etc. | ||
Db is database or assembly name e.g hg17, mm5, rn3 etc. | Db is database or assembly name e.g hg17, mm5, rn3 etc. | ||
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blats will be run in groups of 25 sequences, all | blats will be run in groups of 25 sequences, all | ||
output going to the specified output file. | output going to the specified output file. | ||
[[File:ParseBlatOutput.zip]]: download this file and unzip it. This script parses html output from the BlatBot.pl script and produces either psl output or hyperlinks depending on the BlatBot output type. | |||
usage: parseBlatOutput.pl <output type> <html output> [other html outputs...] | |||
output type is psl or hyperlink | |||
<html output> - file with html returned from blat request | |||
[other html outputs...] - more html file results | |||
output is to stdout | |||
[[Category:User Developed Scripts]] | |||
Latest revision as of 22:50, 13 September 2011
Here is a collection of Blat-related Perl scripts that perform functions that are frequently requested on the genome mailing list. If anyone finds a problem with these scripts then please notify me by selecting the e-mail user link from the side menu bar at: User:Hartera
BlatBot.pl: This is a script that takes a file of FASTA format sequences as input and then submits them to the web-based Blat on the UCSC Genome Browser web site. It obeys the site rules for the number of frequency of hits i.e. Program-driven use of the Genome Browser software is limited to a maximum of one hit every 15 seconds and Blats sequences in batches of 25 sequences at a time.
The script usage is: usage: BlatBot.pl <organism> <db> <searchType> <sortOrder> <input FASTA> <outputType> <output file>
Specify organism using the common name with first letter capitalized.
e.g. Human, Mouse, Rat etc.
Db is database or assembly name e.g hg17, mm5, rn3 etc.
searchType can be BLATGuess, DNA, RNA, transDNA or transRNA
sortOrder can be query,score; query,start; chrom,score;
chrom,start; score.
outputType can be pslNoHeader, psl or hyperlink.
blats will be run in groups of 25 sequences, all
output going to the specified output file.
File:ParseBlatOutput.zip: download this file and unzip it. This script parses html output from the BlatBot.pl script and produces either psl output or hyperlinks depending on the BlatBot output type.
usage: parseBlatOutput.pl <output type> <html output> [other html outputs...]
output type is psl or hyperlink
<html output> - file with html returned from blat request
[other html outputs...] - more html file results
output is to stdout
