Mercurial > repos > blankenberg > data_manager_fetch_genome_all_fasta

annotate tool-data/all_fasta.loc.sample @ 4:357b7bea23ae

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Add missing tool_data_table_conf.xml.sample
author Daniel Blankenberg <dan@bx.psu.edu>
date Fri, 31 May 2013 12:36:25 -0400
parents 6115872b2240
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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6115872b2240 Add Fetch Genome / all_fasta.loc 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
6115872b2240 Add Fetch Genome / all_fasta.loc Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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2 #under the "genome" directory (a directory that contains a directory
6115872b2240 Add Fetch Genome / all_fasta.loc Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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3 #for each build). The script extract_fasta.py will generate the file
6115872b2240 Add Fetch Genome / all_fasta.loc Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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4 #all_fasta.loc. This file has the format (white space characters are
6115872b2240 Add Fetch Genome / all_fasta.loc Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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5 #TAB characters):
6115872b2240 Add Fetch Genome / all_fasta.loc Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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6 #
6115872b2240 Add Fetch Genome / all_fasta.loc Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
6115872b2240 Add Fetch Genome / all_fasta.loc Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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8 #
6115872b2240 Add Fetch Genome / all_fasta.loc Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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9 #So, all_fasta.loc could look something like this:
6115872b2240 Add Fetch Genome / all_fasta.loc Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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10 #
6115872b2240 Add Fetch Genome / all_fasta.loc Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
6115872b2240 Add Fetch Genome / all_fasta.loc Data Manager.
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
6115872b2240 Add Fetch Genome / all_fasta.loc Data Manager.
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
6115872b2240 Add Fetch Genome / all_fasta.loc Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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14 #
6115872b2240 Add Fetch Genome / all_fasta.loc Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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15 #Your all_fasta.loc file should contain an entry for each individual
6115872b2240 Add Fetch Genome / all_fasta.loc Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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16 #fasta file. So there will be multiple fasta files for each build,
6115872b2240 Add Fetch Genome / all_fasta.loc Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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17 #such as with hg19 above.
6115872b2240 Add Fetch Genome / all_fasta.loc Data Manager.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
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18 #