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planemo upload commit 418d3a27a673cef3f350e514fb6101fcde009b9d
author yating-l
date Mon, 06 Nov 2017 15:45:26 -0500
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1 gbToFasta
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2 ==========================================================
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3 Galaxy wrapper for UCSC tools gbToFasta and raToTab. Convert GenBank records to fasta, create TRIX index, and create table with coding regions information for each mRNA record.
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5 gbToFasta
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6 ---------
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8 gbToFaRa - Convert GenBank flat format file to an fa file containing
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9 the sequence data, an ra file containing other relevant info and
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10 a ta file containing summary statistics.
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12 usage:
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13 gbToFaRa filterFile faFile raFile taFile genBankFile(s)
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14 where filterFile is definition of which records and fields
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15 use /dev/null if you want no filtering.
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17 $ gbToFaRa /dev/null gbfile.fa gbfile.ra gbfile.ta gbfile
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19 raToTab
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20 --------
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22 * Create table with coding regions information for each mRNA record
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24 raToTab -cols=acc,cds gbfile.ra gbfile.cds
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27 * Create TRIX index
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29 #. Create search index and metadata
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31 raToTab -cols=acc,def gbfile.ra gbfile.info
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33 #. Create TRIX index
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35 ixIxx gbfile.info gbfile.ix gbfile.ixx
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37 Source code:
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38 ============
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40 http://hgdownload.cse.ucsc.edu/admin/exe/
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42 Licence
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43 -------
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44 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).