Mercurial > repos > dereeper > subseq_protein
comparison extract_proteic_seq_using_coordinates.xml @ 4:621bec1d98ea draft default tip
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| author | dereeper |
|---|---|
| date | Sun, 16 Sep 2012 13:16:45 -0400 |
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| 3:840657df6623 | 4:621bec1d98ea |
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| 1 <tool id="extract_proteic_seq_from_coordinates" name="Extract protein subsequences"> | |
| 2 <description>from FASTA using coordinates</description> | |
| 3 <command interpreter="bash">extract_proteic_seq_using_coordinates.sh $input $output $coordinates</command> | |
| 4 <inputs> | |
| 5 <param format="fasta" name="input" type="data" label="Protein FASTA file"/> | |
| 6 <param format="tabular" name="coordinates" type="data" label="Coordinates for extraction (tabular)"/> | |
| 7 </inputs> | |
| 8 <outputs> | |
| 9 <data format="fasta" name="output" label="Extracted proteins"/> | |
| 10 </outputs> | |
| 11 <help> | |
| 12 | |
| 13 .. class:: infomark | |
| 14 | |
| 15 **Program encapsulated in Galaxy by Southgreen** | |
| 16 | |
| 17 .. class:: infomark | |
| 18 | |
| 19 **extract_proteic_seq_using_coordinates.pl version 1.0, 2012** | |
| 20 | |
| 21 ----- | |
| 22 | |
| 23 ========== | |
| 24 Authors: | |
| 25 ========== | |
| 26 | |
| 27 **Dereeper A** | |
| 28 | |
| 29 ----- | |
| 30 | |
| 31 =========== | |
| 32 Overview: | |
| 33 =========== | |
| 34 | |
| 35 Extract protein subsequences from FASTA file using coordinates. | |
| 36 | |
| 37 | |
| 38 ----- | |
| 39 | |
| 40 **Example** | |
| 41 | |
| 42 If the input dataset is:: | |
| 43 | |
| 44 >MCCS00001-0.9-1 | |
| 45 MRLQLGLRRLHFLRRRDHCNHHRRGFATKYSGRVVVETDNGRSFAVEVDNPILQTDVRGY | |
| 46 PLPRRDLICKVVSILQSPPSTASSSSFDDLFMDLSDYLETLNVMITPSEASEILKSLKSP | |
| 47 NLALKFFQFCSSEIPDFRHNSFTYNRILLILSKAYLPNRLDLVRNILNEMDQSATGGSIS | |
| 48 TVNILIGIFSDGQEYGGIDELEKCLGLVKKWELSLNCYTYKCLMQGYLRLNDSKKALEVY | |
| 49 REMTRRGYKLDIFAYNMLLDALAKDEK | |
| 50 >MCCS00001-0.1-1 | |
| 51 MRLNSRFGTSSLIHVSLVLLLCFKASGGSAERSSAFFIFGDSTVDPGNNNYIKTTPENQA | |
| 52 NYKPYGQNGFFKEPTGRFSDGRIIVDYIAEYAKLPIIPPYLQPSADYSHGVNFASGGAGI | |
| 53 LSTTNPGVVIDLKTQLEYFHKVQRSLAEKLGTAEAEEIISNAVYFISMGSNDYMGGYLGN | |
| 54 PEMQQLHPPEDYVRMVIGNLTQGIQELYDRGARKFGFLSLCPLGCLPALRVLNPKGHDAG | |
| 55 CFEQASALALAHSNALQAVLPNLELLLPKGFKYCNSNFYDWLLDRINDPTKYGFKEGESA | |
| 56 CCGAGPYRGIFTCGGTKKDPNYELCDNPSDYVWFDSFHPTERIHEQFAKALWDGLSPSVG | |
| 57 PYNLEGLFFNKQTIADVVDNPETQQIF | |
| 58 | |
| 59 Interval file must be in the form:: | |
| 60 | |
| 61 MCCS00001-0.9-1 2 6 | |
| 62 MCCS00001-0.1-1 5 132 | |
| 63 | |
| 64 Extracting sequences returns:: | |
| 65 | |
| 66 >MCCS00001-0.9-1 | |
| 67 RLQLG | |
| 68 >MCCS00001-0.1-1 | |
| 69 SRFGTSSLIHVSLVLLLCFKASGGSAERSSAFFIFGDSTVDPGNNNYIKTTPENQANYKP | |
| 70 YGQNGFFKEPTGRFSDGRIIVDYIAEYAKLPIIPPYLQPSADYSHGVNFASGGAGILSTT | |
| 71 NPGVVIDL | |
| 72 | |
| 73 | |
| 74 </help> | |
| 75 </tool> |