Mercurial > repos > yating-l > gbtofasta

annotate README.rst @ 2:cabe1df9d31a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
author yating-l
date Fri, 03 Feb 2017 13:21:33 -0500
parents
children e195691d3e71
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
1 gbToFasta
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
2 ==========================================================
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
3 Galaxy wrapper for UCSC tools gbToFasta and raToTab. Convert GenBank records to fasta and create table with coding regions information for each mRNA record.
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
4
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
5 gbToFasta
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
6 ---------
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
7
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
8 gbToFaRa - Convert GenBank flat format file to an fa file containing
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
9 the sequence data, an ra file containing other relevant info and
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
10 a ta file containing summary statistics.
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
11
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
12 usage:
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
13 gbToFaRa filterFile faFile raFile taFile genBankFile(s)
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
14 where filterFile is definition of which records and fields
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
15 use /dev/null if you want no filtering.
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
16
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
17 $ gbToFaRa /dev/null gbfile.fa gbfile.ra gbfile.ta gbfile
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
18
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
19 raToTab
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
20 --------
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
21 raToTab - Create table with coding regions information for each mRNA record
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
22
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
23 usage:
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
24 raToTab -cols=acc,cds gbfile.ra gbfile.cds
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
25
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
26 Source code:
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
27 ============
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
28
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
29 http://hgdownload.cse.ucsc.edu/admin/exe/
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
30
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
31 Licence
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
32 -------
cabe1df9d31a planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
yating-l
parents:
diff changeset
33 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).