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11
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1 #Your all_fasta.loc file should contain an entry for each individual
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2 #fasta file. So there will be multiple fasta files for each build,
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3 #such as with hg19 above.
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4 #This file lists the locations and dbkeys of all the fasta files
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5 #under the "genome" directory (a directory that contains a directory
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6 #for each build). The script extract_fasta.py will generate the file
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7 #all_fasta.loc. This file has the format (white space characters are
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8 #TAB characters):
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9 #
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10 #<unique_build_id> <dbkey> <display_name> <file_path>
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11 #
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12 #So, all_fasta.loc could look something like this:
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13 #
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14 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
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15 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
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16 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
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17 #
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18 #Your all_fasta.loc file should contain an entry for each individual
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19 #fasta file. So there will be multiple fasta files for each build,
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20 #such as with hg19 above.
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21 #
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22 hgtest hgtest hgtest ${__HERE__}/humsamp.fa
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