Mercurial > repos > bjoern-gruening > glimmer3

<tool id="glimmer3-extract" name="glimmer3-extract" version="0.1">
  <description></description>
  <command > tigr-glimmer extract -t $seqInput $cordInput > $output 2> /dev/null </command>
  <inputs>
	<param name="seqInput" type="data" format="fasta" label="Genome Sequence" help="Dataset missing? See TIP below"/>
	<param name="cordInput" type="data"  label="Coordinates" help="Dataset missing? See TIP below"/>
  </inputs>
  <outputs>
    <data format="fasta" name="output" />
  </outputs>
  <tests>
	<test>
		<param name="seqInput" value='glimmer3/seqTest.fa'/>
		<param name="cordInput" value='glimmer3/cordTest.txt'/>
		<output name="output" file='glimmer3/extractTestOutput.dat'/>
	</test>
 </tests>

<help>

**What it does**

	This program reads a genome sequence and a list of coordinates for it and outputs a multi-
	fasta file of the regions specified by the coordinates.

-----

**Glimmer Overview**

::

**************		**************		**************		**************
*            *		*	     *		*            *		*            *
* long-orfs  *  ===>	*   Extract  *	===>	* build-icm  *  ===>	*  glimmer3  *
*            *		*	     *		*	     *  	*	     *
**************		**************		**************		**************

-----

**Example**


* input ::

	-Genome Sequence

	CELF22B7  C.aenorhabditis elegans (Bristol N2) cosmid F22B7
	GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
	GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
	TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
	TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
	GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
	ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
	AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
	CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
	TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
	AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
	GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
	AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
	CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
	AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
	GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
	...

	- Coorinates

	00001   40137      52  +2   0.892
	00002    1319    1095  -3   0.654
	00003    1555    1391  -2   0.793
	00004    1953    2066  +3   1.078
	00005    2045    2146  +2   0.919
	00006    4463    4759  +2   0.985
	00007    6785    6582  -3   1.033
	00008    6862    7020  +1   0.915
	00009    7300    7488  +1   0.900
	00010    7463    7570  +2   0.912
	00011    8399    8527  +2   1.044
	00012   10652   10545  -3   0.895
	00013   12170   12066  -3   1.108
	00014   13891   13748  -2   0.998
	00015   14157   14044  -1   1.026
	00016   15285   15410  +3   0.928
	00017   15829   15704  -2   0.949
	...

* output::

		>00001  40137 52  len=135
		ATGACACATTTGCTCGTTGCTTTGACCCACTACGAGGCCAGTATCATGATTTCTAGAAAA
		ACCCTCTTTTTGACTTCTTCCTCCATGATCCTTGTAGATTTTGAATTTGAAGTTTTTTCT
		CATTCCAAAACTCTG

		>00002  1319 1095  len=222
		TTGGCTCGCCGTTTTGGAGTCCGTGCTGGAATGCCTGGCTTCATCTCAAATAAACTTTGT
		CCGAGTCTAACGATTGTTCCAGGAAATTACCCTAAATACACTAAAGTCAGTCGCCAATTT
		TCACAAATTTTCATGGAATACGATTCGGATGTTGGAATGATGTCATTGGATGAGGCATTT
		ATAGATTTGACAGACTATGTGGCAAGTAATACAGAAAAAAGT

		>00003  1555 1391  len=162
		ATGGAGAATCTTGAGATGAAACTGGAATCATCTAGAGATTTATCAAGAGACTGTGTTTGT
		ATAGATATGGATGCTTATTTTGCCGCAGTTGAAATGAGAGATAATCCTGCACTGAGAACA
		GTTCCTATGGCCGTAGGCTCATCGGCAATGCTGGTAAGCACC

		>00004  1953 2066  len=111
		GTGCGCGAGAAAAAACTACGCGTTAACCGCCAATTTTCACTTCCCCACAGATCTGTCTCG
		AGATTCTCGAGTCATTTTTCAAGTTTATTTGTTTGTCAGCGGTTGTTTTAT
		.....

-------

**References**

A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007).


 </help>

</tool>
author	bjoern-gruening
date	Wed, 11 Jan 2012 09:34:45 -0500
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