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author dereeper
date Sun, 16 Sep 2012 13:16:45 -0400
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<tool id="extract_proteic_seq_from_coordinates" name="Extract protein subsequences">
	<description>from FASTA using coordinates</description>
	<command interpreter="bash">extract_proteic_seq_using_coordinates.sh $input $output $coordinates</command>
	<inputs>
		<param format="fasta" name="input" type="data" label="Protein FASTA file"/>
		<param format="tabular" name="coordinates" type="data" label="Coordinates for extraction (tabular)"/>
	</inputs>
	<outputs>
		<data format="fasta" name="output" label="Extracted proteins"/>
	</outputs>
	<help>
	
.. class:: infomark

**Program encapsulated in Galaxy by Southgreen**

.. class:: infomark

**extract_proteic_seq_using_coordinates.pl version 1.0, 2012**

-----

==========
 Authors:
==========

**Dereeper A**

-----

===========
 Overview:
===========

Extract protein subsequences from FASTA file using coordinates.  


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**Example**

If the input dataset is::

	>MCCS00001-0.9-1
	MRLQLGLRRLHFLRRRDHCNHHRRGFATKYSGRVVVETDNGRSFAVEVDNPILQTDVRGY
	PLPRRDLICKVVSILQSPPSTASSSSFDDLFMDLSDYLETLNVMITPSEASEILKSLKSP
	NLALKFFQFCSSEIPDFRHNSFTYNRILLILSKAYLPNRLDLVRNILNEMDQSATGGSIS
	TVNILIGIFSDGQEYGGIDELEKCLGLVKKWELSLNCYTYKCLMQGYLRLNDSKKALEVY
	REMTRRGYKLDIFAYNMLLDALAKDEK
	>MCCS00001-0.1-1
	MRLNSRFGTSSLIHVSLVLLLCFKASGGSAERSSAFFIFGDSTVDPGNNNYIKTTPENQA
	NYKPYGQNGFFKEPTGRFSDGRIIVDYIAEYAKLPIIPPYLQPSADYSHGVNFASGGAGI
	LSTTNPGVVIDLKTQLEYFHKVQRSLAEKLGTAEAEEIISNAVYFISMGSNDYMGGYLGN
	PEMQQLHPPEDYVRMVIGNLTQGIQELYDRGARKFGFLSLCPLGCLPALRVLNPKGHDAG
	CFEQASALALAHSNALQAVLPNLELLLPKGFKYCNSNFYDWLLDRINDPTKYGFKEGESA
	CCGAGPYRGIFTCGGTKKDPNYELCDNPSDYVWFDSFHPTERIHEQFAKALWDGLSPSVG
	PYNLEGLFFNKQTIADVVDNPETQQIF

Interval file must be in the form::

	MCCS00001-0.9-1	2	6
	MCCS00001-0.1-1	5	132

Extracting sequences returns::

	>MCCS00001-0.9-1
	RLQLG
	>MCCS00001-0.1-1
	SRFGTSSLIHVSLVLLLCFKASGGSAERSSAFFIFGDSTVDPGNNNYIKTTPENQANYKP
	YGQNGFFKEPTGRFSDGRIIVDYIAEYAKLPIIPPYLQPSADYSHGVNFASGGAGILSTT
	NPGVVIDL


	</help>
</tool>