annotate all_fasta.loc.sample @ 0:f28df61581f4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
author iuc
date Fri, 09 Dec 2022 17:40:40 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the fasta files
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
5 #TAB characters):
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
6 #
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
7 #<unique_build_id> <dbkey> <display_name> <file_path>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
8 #
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
10 #
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
14 #
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
17 #such as with hg19 above.
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
18 #