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Create data_manager_fetch_genome_dbkeys_all_fasta.
author Daniel Blankenberg <dan@bx.psu.edu>
date Wed, 02 Jul 2014 00:35:38 -0400
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d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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1 #This file lists the locations and dbkeys of all the fasta files
d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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2 #under the "genome" directory (a directory that contains a directory
d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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3 #for each build). The script extract_fasta.py will generate the file
d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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4 #all_fasta.loc. This file has the format (white space characters are
d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
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5 #TAB characters):
d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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6 #
d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
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8 #
d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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9 #So, all_fasta.loc could look something like this:
d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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10 #
d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
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14 #
d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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15 #Your all_fasta.loc file should contain an entry for each individual
d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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16 #fasta file. So there will be multiple fasta files for each build,
d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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17 #such as with hg19 above.
d59e1d23b388 Create data_manager_fetch_genome_dbkeys_all_fasta.
Daniel Blankenberg <dan@bx.psu.edu>
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18 #