annotate tool-data/all_fasta.loc.sample @ 9:57867d1931d6 draft

planemo upload for repository https://github.com/fubar2/microsatbed commit 6e9d6a1dd5b8615dfa80b1b239e22b266c00a6dd
author fubar
date Tue, 13 Aug 2024 05:31:37 +0000
parents 4ff60fb9ca4d
children e2e1e48a2e56
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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 #