[2] | 1 | This file explains how to create annotation indexes for the annotation profiler tool. Annotation profiler indexes are an exceedingly simple binary format, |
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| 2 | containing no header information and consisting of an ordered linear list of (start,stop encoded individually as '<I') regions which are covered by a UCSC table partitioned |
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| 3 | by chromosome name. Genomic regions are merged by overlap / direct adjacency (e.g. a table having ranges of: 1-10, 6-12, 12-20 and 25-28 results in two merged ranges of: 1-20 and 25-28). |
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| 4 | |
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| 5 | Files are arranged like: |
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| 6 | /profiled_annotations/DBKEY/TABLE_NAME/ |
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| 7 | CHROMOSOME_NAME.covered |
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| 8 | CHROMOSOME_NAME.total_coverage |
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| 9 | CHROMOSOME_NAME.total_regions |
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| 10 | /profiled_annotations/DBKEY/ |
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| 11 | DBKEY_tables.xml |
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| 12 | chromosomes.txt |
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| 13 | profiled_info.txt |
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| 14 | |
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| 15 | |
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| 16 | where CHROMOSOME_NAME.covered is the binary file, CHROMOSOME_NAME.total_coverage is a text file containing the integer count of bases covered by the |
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| 17 | table and CHROMOSOME_NAME.total_regions contains the integer count of the number of regions found in CHROMOSOME_NAME.covered |
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| 18 | |
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| 19 | DBKEY_tables.xml should be appended to the annotation profile available table configuration file (tool-data/annotation_profiler_options.xml). |
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| 20 | The DBKEY should also be added as a new line to the annotation profiler valid builds file (annotation_profiler_valid_builds.txt). |
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| 21 | The output (/profiled_annotations/DBKEY) should be made available as GALAXY_ROOT/tool-data/annotation_profiler/DBKEY. |
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| 22 | |
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| 23 | profiled_info.txt contains info on the generated annotations, separated by lines with tab-delimited label,value pairs: |
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| 24 | profiler_version - the version of the build_profile_indexes.py script that was used to generate the profiled data |
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| 25 | dbkey - the dbkey used for the run |
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| 26 | chromosomes - contains the names and lengths of chromosomes that were used to parse single-chromosome tables (tables divided into individual files by chromosome) |
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| 27 | dump_time - the declared dump time of the database, taken from trackDb.txt.gz |
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| 28 | profiled_time - seconds since epoch in utc for when the database dump was profiled |
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| 29 | database_hash - a md5 hex digest of all the profiled table info |
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| 30 | |
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| 31 | |
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| 32 | Typical usage includes: |
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| 33 | |
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| 34 | python build_profile_indexes.py -d hg19 -i /ucsc_data/hg19/database/ > hg19.txt |
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| 35 | |
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| 36 | where the genome build is hg19 and /ucsc_data/hg19/database/ contains the downloaded database dump from UCSC (e.g. obtained by rsync: rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ /ucsc_data/hg19/database/). |
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| 37 | |
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| 38 | |
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| 39 | |
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| 40 | By default, chromosome names come from a file named 'chromInfo.txt.gz' found in the input directory, with FTP used as a backup. |
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| 41 | When FTP is used to obtain the names of chromosomes from UCSC for a particular genome build, alternate ftp sites and paths can be specified by using the --ftp_site and --ftp_path attributes. |
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| 42 | Chromosome names can instead be provided on the commandline via the --chromosomes option, which accepts a comma separated list of:ChromName1[=length],ChromName2[=length],... |
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| 43 | |
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| 44 | |
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| 45 | |
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| 46 | usage = "usage: %prog options" |
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| 47 | parser = OptionParser( usage=usage ) |
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| 48 | parser.add_option( '-d', '--dbkey', dest='dbkey', default='hg18', help='dbkey to process' ) |
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| 49 | parser.add_option( '-i', '--input_dir', dest='input_dir', default=os.path.join( 'golden_path','%s', 'database' ), help='Input Directory' ) |
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| 50 | parser.add_option( '-o', '--output_dir', dest='output_dir', default=os.path.join( 'profiled_annotations','%s' ), help='Output Directory' ) |
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| 51 | parser.add_option( '-c', '--chromosomes', dest='chromosomes', default='', help='Comma separated list of: ChromName1[=length],ChromName2[=length],...' ) |
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| 52 | parser.add_option( '-b', '--bitset_size', dest='bitset_size', default=DEFAULT_BITSET_SIZE, type='int', help='Default BitSet size; overridden by sizes specified in chromInfo.txt.gz or by --chromosomes' ) |
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| 53 | parser.add_option( '-f', '--ftp_site', dest='ftp_site', default='hgdownload.cse.ucsc.edu', help='FTP site; used for chromosome info when chromInfo.txt.gz method fails' ) |
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| 54 | parser.add_option( '-p', '--ftp_path', dest='ftp_path', default='/goldenPath/%s/chromosomes/', help='FTP Path; used for chromosome info when chromInfo.txt.gz method fails' ) |
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