Mercurial > repos > yating-l > gbtofasta

gbToFasta
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Galaxy wrapper for UCSC tools gbToFasta and raToTab. Convert GenBank records to fasta and create table with coding regions information for each mRNA record.

gbToFasta
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gbToFaRa - Convert GenBank flat format file to an fa file containing
the sequence data, an ra file containing other relevant info and
a ta file containing summary statistics.

usage:
  gbToFaRa filterFile faFile raFile taFile genBankFile(s)
  where filterFile is definition of which records and fields
  use /dev/null if you want no filtering.

  $ gbToFaRa /dev/null gbfile.fa gbfile.ra gbfile.ta gbfile

raToTab
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raToTab - Create table with coding regions information for each mRNA record

usage:
  raToTab -cols=acc,cds gbfile.ra gbfile.cds

Source code:
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http://hgdownload.cse.ucsc.edu/admin/exe/

Licence
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Please note that commercial download and installation of the Blat and In-Silico PCR software may be licensed through Kent Informatics (http://www.kentinformatics.com).
author	yating-l
date	Mon, 05 Jun 2017 12:00:08 -0400
parents	cabe1df9d31a
children	e195691d3e71