view extract_proteic_seq_using_coordinates.xml @ 0:60507a6de56c draft

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<tool id="extract_proteic_seq_from_coordinates" name="Extract protein sequences">
	<description>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="txt" name="coordinates" type="data" label="Coordinates for extraction"/>
	</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**

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==========
 Authors:
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**Dereeper A**

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===========
 Overview:
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Extract sequences from a protein 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>