Mercurial > repos > fubar > jbrowse2

annotate all_fasta.loc.sample @ 57:94264fe60478 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
author fubar
date Thu, 21 Mar 2024 08:01:42 +0000
parents c60b17456297
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
10
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the fasta files
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
5 #TAB characters):
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
6 #
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
7 #<unique_build_id> <dbkey> <display_name> <file_path>
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
8 #
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
10 #
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
14 #
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
17 #such as with hg19 above.
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
diff changeset
18 #