Mercurial > repos > mvdbeek > get_reference_fasta

annotate tool-data/all_fasta.loc.sample @ 0:b5c0b28cdfb3 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
author mvdbeek
date Thu, 25 Feb 2016 07:19:45 -0500
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b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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1 #This file lists the locations and dbkeys of all the fasta files
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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2 #under the "genome" directory (a directory that contains a directory
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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3 #for each build). The script extract_fasta.py will generate the file
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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4 #all_fasta.loc. This file has the format (white space characters are
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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5 #TAB characters):
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
parents:
diff changeset
6 #
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
parents:
diff changeset
8 #
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
parents:
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9 #So, all_fasta.loc could look something like this:
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
parents:
diff changeset
10 #
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
parents:
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
parents:
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
parents:
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
parents:
diff changeset
14 #
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
parents:
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16 #fasta file. So there will be multiple fasta files for each build,
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
parents:
diff changeset
17 #such as with hg19 above.
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
parents:
diff changeset
18 #