Mercurial > repos > ieguinoa > load_ref_data
changeset 1:cccb98962d4c draft default tip
Uploaded
| author | ieguinoa |
|---|---|
| date | Tue, 25 May 2021 22:03:31 +0000 |
| parents | faeb871ac76d |
| children | |
| files | tool-data/all_fasta.loc.sample tool-data/all_gff.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 25 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Tue May 25 22:03:31 2021 +0000 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_gff.loc.sample Tue May 25 22:03:31 2021 +0000 @@ -0,0 +1,3 @@ +#The all_gff.loc file has this format: +# +#<unique_build_id> <dbkey> <display_name> <path_to_gff_file>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue May 25 22:03:31 2021 +0000 @@ -0,0 +1,4 @@ +<tables> + <table name="all_gff" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/all_gff.loc" /> </table> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"><columns>value, dbkey, name, path</columns><file path="tool-data/all_fasta.loc" /></table> +</tables>