Mercurial > repos > cpt > cpt_convert_mga

comparison all_fasta.loc.sample @ 13:c62acc3e4bf6 draft

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planemo upload commit 852ac96ca53a2ffa0947e6df5e24671866b642f5
author cpt
date Sat, 22 Jul 2023 17:15:42 +0000
parents 9c03867832fc
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12:9c03867832fc 13:c62acc3e4bf6
1 <!-- not a real sample --> 1 #This file lists the locations and dbkeys of all the fasta files
2 <tables> 2 #under the "genome" directory (a directory that contains a directory
3 <!-- Locations of all fasta files under genome directory --> 3 #for each build). The script extract_fasta.py will generate the file
4 <table name="all_fasta" comment_char="#"> 4 #all_fasta.loc. This file has the format (white space characters are
5 <columns>value, dbkey, name, path</columns> 5 #TAB characters):
6 <file path="tool-data/all_fasta.loc" /> 6 #
7 </table> 7 #<unique_build_id> <dbkey> <display_name> <file_path>
8 </tables> 8 #
9 #So, all_fasta.loc could look something like this:
10 #
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
14 #
15 #Your all_fasta.loc file should contain an entry for each individual
16 #fasta file. So there will be multiple fasta files for each build,
17 #such as with hg19 above.
18 #