annotate tool-data/all_fasta.loc.sample @ 3:d25dc80a6a61 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta commit 40b5e586ec4445e121779ce0e0ededf74ed356f7
author artbio
date Sun, 15 Oct 2023 13:34:58 +0000
parents 816bedbb305c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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1 #This file lists the locations and dbkeys of all the fasta files
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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2 #under the "genome" directory (a directory that contains a directory
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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3 #for each build). The script extract_fasta.py will generate the file
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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4 #all_fasta.loc. This file has the format (white space characters are
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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5 #TAB characters):
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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6 #
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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8 #
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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9 #So, all_fasta.loc could look something like this:
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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10 #
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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14 #
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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15 #Your all_fasta.loc file should contain an entry for each individual
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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16 #fasta file. So there will be multiple fasta files for each build,
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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17 #such as with hg19 above.
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
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18 #