cleanup

README.md

@@ -61,38 +61,3 @@ The Documentation about the different classes can be found [here](https://physcr
 
 There are some tests [here](./test/) and [here](./ws-test/), which test the major functionality of the code. If you want to test if the code works on your machine, please run `python tests/testfilesetup.py` and then `sh tests/run_test.sh`,  `sh ws-tests/run_ws-tests.sh`.
 
-
-### Notes to self
-
-rsync -av ftp.ncbi.nih.gov::pub/taxonomy/gi_taxid_nucl.dmp.gz gi_taxid_nucl.dmp.gz
-gunzip /home/ejmctavish/ncbi/gi_taxid_nucl.dmp.gz
-
-wget http://purl.org/opentree/ott/ott2.9/ott2.9.tgz 
-
-tar -zxvf ott2.9.tgz 
-
-
-wget files.opentreeoflife.org/ott/ott3.0/ott3.0.tgz
-tar -xzvf ott3.0.tgz
-
-grep ncbi: ../ott3.0/taxonomy.tsv | sed -E -e "s/([0-9]+).+?\|.+?\|(.+?)\|.+?\|.*ncbi:([0-9]+).*/\\1,\\3,\\2/" > ott_ncbi
-
-OR
-
-grep ncbi: ott3.0/taxonomy.tsv | sed -r -e "s/([0-9]+).+?\|.+?\|(.+?)\|.+?\|.*ncbi:([0-9]+).*/\\1,\\3,\\2/" > physcraper/taxonomy/ott_ncbi
-
-RSYNC_COMMAND=$(s.system("rsync -av ftp.ncbi.nih.gov::pub/taxonomy/gi_taxid_nucl.dmp.gz {}.gz".format(self.config.ncbi_dmp))
-os.system("tar -xzvf {}.gz".format(self.config.ncbi_dmp)))
-
-    if [ $? -eq 0 ]; then
-        # Success do some more work!
-
-        if [ -n "${RSYNC_COMMAND}" ]; then
-            # Stuff to run, because rsync has changes
-        else
-            # No changes were made by rsync
-        fi
-    else
-        # Something went wrong!
-        exit 1
-    fi