Mercurial > repos > iuc > jvarkit_wgscoverageplotter
annotate tool-data/all_fasta.loc.sample @ 3:ac048a34cac3 draft default tip
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit 7224953c0b42f43a91dc76ee1015f355a311b391"
| author | iuc | 
|---|---|
| date | Fri, 12 Feb 2021 12:55:56 +0000 | 
| parents | 70efe7b19018 | 
| children | 
| rev | line source | 
|---|---|
| 
2
 
70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
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1 #This file lists the locations and dbkeys of all the fasta files | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
 | 
2 #under the "genome" directory (a directory that contains a directory | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
 | 
3 #for each build). The script extract_fasta.py will generate the file | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
 | 
4 #all_fasta.loc. This file has the format (white space characters are | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
 | 
5 #TAB characters): | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
 | 
6 # | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
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7 #<unique_build_id> <dbkey> <display_name> <file_path> | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
 | 
8 # | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
 | 
9 #So, all_fasta.loc could look something like this: | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
 | 
10 # | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
 | 
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
 | 
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
 | 
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
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14 #sars-cov-2 SARS-CoV-2 SARS-CoV-2 (MN908947.3) /depot/data/MN908947_3_Wuhan-Hu-1.fasta | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
 | 
15 # | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
 | 
16 #Your all_fasta.loc file should contain an entry for each individual | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
 | 
17 #fasta file. So there will be multiple fasta files for each build, | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
 | 
18 #such as with hg19 above. | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
 | 
19 # | 
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70efe7b19018
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit dd0745115487da9c9e9f51c7049619263a055b8e"
 
iuc 
parents:  
diff
changeset
 | 
20 # | 
