Mercurial > repos > morinlab > mutationseq

annotate tool-data/all_fasta.loc.sample @ 0:3f5545f5f0c8 draft

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planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
author morinlab
date Tue, 11 Oct 2016 14:21:25 -0400
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3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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1 #This file lists the locations and dbkeys of all the fasta files
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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2 #under the "genome" directory (a directory that contains a directory
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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3 #for each build). The script extract_fasta.py will generate the file
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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4 #all_fasta.loc. This file has the format (white space characters are
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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5 #TAB characters):
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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6 #
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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8 #
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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9 #So, all_fasta.loc could look something like this:
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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10 #
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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14 #
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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15 #Your all_fasta.loc file should contain an entry for each individual
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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16 #fasta file. So there will be multiple fasta files for each build,
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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17 #such as with hg19 above.
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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18 #