Mercurial > repos > iuc > microsatbed

annotate test-data/all_fasta.loc @ 4:5f8efb080f49 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 891fc6321cd94c9a63c880d75989d79521f1a9b6
author iuc
date Sat, 14 Sep 2024 12:17:02 +0000
parents 2b970db61912
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
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1 #Your all_fasta.loc file should contain an entry for each individual
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
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diff changeset
2 #fasta file. So there will be multiple fasta files for each build,
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
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3 #such as with hg19 above.
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
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4 #This file lists the locations and dbkeys of all the fasta files
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
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5 #under the "genome" directory (a directory that contains a directory
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
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diff changeset
6 #for each build). The script extract_fasta.py will generate the file
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
parents:
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7 #all_fasta.loc. This file has the format (white space characters are
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
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diff changeset
8 #TAB characters):
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
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9 #
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
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10 #<unique_build_id> <dbkey> <display_name> <file_path>
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
parents:
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11 #
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
parents:
diff changeset
12 #So, all_fasta.loc could look something like this:
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
parents:
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13 #
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
parents:
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14 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
parents:
diff changeset
15 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
parents:
diff changeset
16 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
parents:
diff changeset
17 #
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
parents:
diff changeset
18 #Your all_fasta.loc file should contain an entry for each individual
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
parents:
diff changeset
19 #fasta file. So there will be multiple fasta files for each build,
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
parents:
diff changeset
20 #such as with hg19 above.
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
parents:
diff changeset
21 #
2b970db61912 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
iuc
parents:
diff changeset
22 hgtest hgtest hgtest ${__HERE__}/humsamp.fa