Mercurial > repos > fubar > microsatbedfubar
annotate tool-data/all_fasta.loc.sample @ 10:43a8165cec3a draft
planemo upload for repository https://github.com/fubar2/microsatbed commit 6e9d6a1dd5b8615dfa80b1b239e22b266c00a6dd-dirty
author | fubar |
---|---|
date | Tue, 13 Aug 2024 05:33:14 +0000 |
parents | 4ff60fb9ca4d |
children | e2e1e48a2e56 |
rev | line source |
---|---|
0
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
1 #This file lists the locations and dbkeys of all the fasta files |
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
2 #under the "genome" directory (a directory that contains a directory |
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
3 #for each build). The script extract_fasta.py will generate the file |
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
4 #all_fasta.loc. This file has the format (white space characters are |
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
5 #TAB characters): |
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
6 # |
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
7 #<unique_build_id> <dbkey> <display_name> <file_path> |
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
8 # |
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
9 #So, all_fasta.loc could look something like this: |
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
10 # |
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa |
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa |
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa |
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
14 # |
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
15 #Your all_fasta.loc file should contain an entry for each individual |
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
16 #fasta file. So there will be multiple fasta files for each build, |
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
17 #such as with hg19 above. |
4ff60fb9ca4d
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff
changeset
|
18 # |