Mercurial > repos > blankenberg > data_manager_bwa_index_builder
annotate tool-data/all_fasta.loc.sample @ 2:fe6508204acc default tip
Add abspath value translation to data_manager_conf.xml.
| author | Daniel Blankenberg <dan@bx.psu.edu> |
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| date | Tue, 04 Jun 2013 14:57:17 -0400 |
| parents | 11e84434ae70 |
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| rev | line source |
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11e84434ae70
Create bwa indexer data manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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1 #This file lists the locations and dbkeys of all the fasta files |
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11e84434ae70
Create bwa indexer data manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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2 #under the "genome" directory (a directory that contains a directory |
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11e84434ae70
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Daniel Blankenberg <dan@bx.psu.edu>
parents:
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3 #for each build). The script extract_fasta.py will generate the file |
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11e84434ae70
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Daniel Blankenberg <dan@bx.psu.edu>
parents:
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4 #all_fasta.loc. This file has the format (white space characters are |
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11e84434ae70
Create bwa indexer data manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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5 #TAB characters): |
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11e84434ae70
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Daniel Blankenberg <dan@bx.psu.edu>
parents:
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6 # |
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11e84434ae70
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parents:
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7 #<unique_build_id> <dbkey> <display_name> <file_path> |
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Daniel Blankenberg <dan@bx.psu.edu>
parents:
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8 # |
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11e84434ae70
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parents:
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9 #So, all_fasta.loc could look something like this: |
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11e84434ae70
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Daniel Blankenberg <dan@bx.psu.edu>
parents:
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10 # |
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Daniel Blankenberg <dan@bx.psu.edu>
parents:
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa |
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11e84434ae70
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Daniel Blankenberg <dan@bx.psu.edu>
parents:
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa |
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11e84434ae70
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Daniel Blankenberg <dan@bx.psu.edu>
parents:
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa |
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11e84434ae70
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Daniel Blankenberg <dan@bx.psu.edu>
parents:
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14 # |
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11e84434ae70
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Daniel Blankenberg <dan@bx.psu.edu>
parents:
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15 #Your all_fasta.loc file should contain an entry for each individual |
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11e84434ae70
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Daniel Blankenberg <dan@bx.psu.edu>
parents:
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16 #fasta file. So there will be multiple fasta files for each build, |
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Daniel Blankenberg <dan@bx.psu.edu>
parents:
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17 #such as with hg19 above. |
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parents:
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18 # |