Mercurial > repos > jeremyjliu > region_motif_data_manager
changeset 3:8bf194e522bf draft
Uploaded
| author | jeremyjliu |
|---|---|
| date | Sun, 11 Jan 2015 20:40:09 -0500 |
| parents | d5faf2b51b07 |
| children | 75d825e1b00d |
| files | data_manager/test.py tool-data/all_fasta.loc.sample tool-data/motif_databases.loc.sample |
| diffstat | 3 files changed, 9 insertions(+), 31 deletions(-) [+] |
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--- a/data_manager/test.py Sun Jan 11 20:30:46 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -#!/usr/bin/env python -import optparse - -def main(): - #Parse Command Line - parser = optparse.OptionParser() - parser.add_option( '-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description' ) - (options, args) = parser.parse_args() - - filename = args[0] - print(args) - -main() \ No newline at end of file
--- a/tool-data/all_fasta.loc.sample Sun Jan 11 20:30:46 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -#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/motif_databases.loc.sample Sun Jan 11 20:40:09 2015 -0500 @@ -0,0 +1,9 @@ +# +#<value> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#test Test Pouya Subset (hg19) /<path_to_galaxy>/tool-data/motifs/pouya_test_motifs.bed.bgz +#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 +#