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annotate tool-data/all_fasta.loc.sample @ 9:532a336a14c1 default tip

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Need all_fasta.loc for cummerbund
author Jim Johnson <jj@umn.edu>
date Mon, 13 Oct 2014 09:39:39 -0500
parents 57c13cd32044
children
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57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the fasta files
57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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5 #TAB characters):
57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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6 #
57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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8 #
57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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9 #So, all_fasta.loc could look something like this:
57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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10 #
57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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14 #
57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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15 #Your all_fasta.loc file should contain an entry for each individual
57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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16 #fasta file. So there will be multiple fasta files for each build,
57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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17 #such as with hg19 above.
57c13cd32044 Add tool-data/all_fasta.loc.sample for cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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18 #