annotate all_fasta.loc.sample @ 11:c39202869825 draft

planemo upload for repository https://github.com/fubar2/microsatbed commit bfb57ff3a931bc3f3d3549707f7bcf1f561c84c6
author fubar
date Tue, 13 Aug 2024 05:57:05 +0000
parents 12753df8dbb3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
12753df8dbb3 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
12753df8dbb3 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
12753df8dbb3 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
12753df8dbb3 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
12753df8dbb3 planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
5 #TAB characters):
12753df8dbb3 planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
6 #
12753df8dbb3 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>
12753df8dbb3 planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
8 #
12753df8dbb3 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:
12753df8dbb3 planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
10 #
12753df8dbb3 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
12753df8dbb3 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
12753df8dbb3 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
12753df8dbb3 planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
14 #
12753df8dbb3 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
12753df8dbb3 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,
12753df8dbb3 planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
17 #such as with hg19 above.
12753df8dbb3 planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
18 #