Mercurial > repos > artbio > get_reference_fasta
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 |
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date | Sun, 15 Oct 2023 13:34:58 +0000 |
parents | 816bedbb305c |
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816bedbb305c
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
parents:
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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
parents:
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changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
|
8 # |
816bedbb305c
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
parents:
diff
changeset
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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
parents:
diff
changeset
|
10 # |
816bedbb305c
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
artbio
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
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18 # |