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annotate tool-data/all_fasta.loc.sample @ 7:e32aac2299fb draft

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"planemo upload commit 401528f2dba371d4ca2491aaa83e0b2bfe36f81a"
author iuc
date Fri, 15 Nov 2019 08:19:05 -0500
parents 0aa87d97847f
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
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1 #This file lists the locations and dbkeys of all the fasta files
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
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2 #under the "genome" directory (a directory that contains a directory
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
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3 #for each build). The script extract_fasta.py will generate the file
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
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4 #all_fasta.loc. This file has the format (white space characters are
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
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5 #TAB characters):
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6 #
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
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8 #
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
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9 #So, all_fasta.loc could look something like this:
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
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10 #
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
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14 #
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
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15 #Your all_fasta.loc file should contain an entry for each individual
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
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16 #fasta file. So there will be multiple fasta files for each build,
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
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17 #such as with hg19 above.
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
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18 #