Commits

Author Commit Message Labels Comments Date
Giovanni Marco Dall'Olio
Merged in yzhou/ucsc-fetch (pull request #1) Add support for using UCSC session
yzhou
add session support in README.rst
yzhou
add session support in README.rst
yzhou
support using UCSC session
Giovanni Marco Dall'Olio
PARAMS: no need to hard-code the hg assembly id in the default URL
Giovanni Marco Dall'Olio
SPACE: fixed region and parameters for genotype_space. Added the Gaps tracks, which is useful for filtering regions out
Giovanni Marco Dall'Olio
PARAMS: whole genome hg19 coordinates gawk "{print $1, \"human hg19\", NR, 0, $2}" chrom.sizes.hg19 > params/regions/all_chromosomes_hg19.txt
Giovanni Marco Dall'Olio
SPACE: parameters for checking the genotype space project python fetch_ucsc.py -r params/regions/example1.txt -t params/tracks_options/genotype_space.txt -u params/browser_config/genotypespace_ibe.txt -l 1x1
Giovanni Marco Dall'Olio
FETCH: implemented UCSC track HUBS
Giovanni Marco Dall'Olio
DATA: imported chromosome sizes for hg 19 fetchChromSizes hg19 > chrom.sizes
Giovanni Marco Dall'Olio
MINOR: connected account to masterbranch mb:50809d57-1945-4a3b-a0bd-a391f0aa921d https://masterbranch.com/dalloliogm
Giovanni Marco Dall'Olio
REFACT: generalized previous change. get_gene_coords.py can accept an argument if no -g is specified
Giovanni Marco Dall'Olio
REFACT: added a "database" option to get_gene_coords, and provided a better interface
Giovanni Marco Dall'Olio
ADD: a sample tracks config file, to show only the RefGene track on hg18/hg19
Giovanni Marco Dall'Olio
FIX: DOCS: fixed headers in example region files
Giovanni Marco Dall'Olio
DOCS: updated examples, using the --title option
Giovanni Marco Dall'Olio
ADD: new parameter "title", to define a title for the analysis
Giovanni Marco Dall'Olio
DOCS: updated example1, removing iHS
Giovanni Marco Dall'Olio
FIX: reduced header's size in stylesheet
Giovanni Marco Dall'Olio
FIX: fixed doctest example
Giovanni Marco Dall'Olio
ADD: stub for a regions2bed function
Giovanni Marco Dall'Olio
DOCS: cleaning
Giovanni Marco Dall'Olio
PARAMS: adapted stylesheet to rst2pdf 0.16
Giovanni Marco Dall'Olio
DOCS: debugging message
Giovanni Marco Dall'Olio
ADD: position field to regions dictionary. FIX: preserving order of regions in the report file, if sort==False
Giovanni Marco Dall'Olio
DOCS: fixed typo in drosophila example
Giovanni Marco Dall'Olio
DOCS: ADD: updated makefile and examples
Giovanni Marco Dall'Olio
DOCS: ADD: renamed files for example1
Giovanni Marco Dall'Olio
REFACT: intermediary pdf files are saved with a suffix that includes the parameters used to download them
Giovanni Marco Dall'Olio
DOCS: renamed some examples
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