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Convert everything from elementtree to stdlib xml module.

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This commit is contained in:
Dannon Baker
2015-01-29 16:10:56 -05:00
parent ec3eec5609
commit dba89dff83
24 changed files with 68 additions and 86 deletions
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scripts/loc_files/create_all_fasta_loc.py
+2 -2
View File
@@ -1,5 +1,5 @@
import optparse, os, sys
import elementtree.ElementTree as etree
from xml.etree.ElementTree import parse
"""
Generates a loc file containing names of all the fasta files that match the
@@ -212,7 +212,7 @@ def __main__():
# get column names
col_values = []
loc_path = None
tree = etree.parse( options.data_table_xml )
tree = parse( options.data_table_xml )
tables = tree.getroot()
for table in tables.getiterator():
name = table.attrib.get( 'name' )
scripts/microbes/ncbi_to_ucsc.py
+16 -16
View File
@@ -7,7 +7,7 @@ Uses UCSC Archaea DSN.
import sys, os
import urllib
from elementtree import ElementTree
from xml.etree import ElementTree
from BeautifulSoup import BeautifulSoup
from shutil import move
@@ -17,7 +17,7 @@ def __main__():
base_dir = sys.argv[1]
except:
print "using default base_dir:", base_dir
organisms = {}
for result in os.walk(base_dir):
this_base_dir,sub_dirs,files = result
@@ -76,7 +76,7 @@ def __main__():
org_page.pop(0)
if org_page[-1]=="":
org_page.pop(-1)
for row in org_page:
chr = row.split("</a>")[0].split(">")[-1]
refseq = row.split("</a>")[-2].split(">")[-1]
@@ -87,20 +87,20 @@ def __main__():
builds[org]={'chrs':{},'build':build}
builds[org]['chrs'][refseq]=chr
#print build,org,chr,refseq
print
ext_to_edit = ['bed', 'info', ]
for org in builds:
print org,"changed to",builds[org]['build']
#org info file
info_file_old = os.path.join(base_dir+org,org+".info")
info_file_new = os.path.join(base_dir+org,builds[org]['build']+".info")
old_dir = base_dir+org
new_dir = base_dir+builds[org]['build']
#open and edit org info file
info_file_contents = open(info_file_old).read()
info_file_contents = info_file_contents+"build="+builds[org]['build']+"\n"
@@ -114,31 +114,31 @@ def __main__():
old_name = os.path.join(this_base_dir,file)
new_name = os.path.join(this_base_dir,builds[org]['chrs'][chrom]+file[len(chrom):])
move(old_name,new_name)
#edit contents of file, skiping those in list
if file.split(".")[-1] not in ext_to_edit: continue
file_contents = open(new_name).read()
file_contents = file_contents.replace(chrom,builds[org]['chrs'][chrom])
#special case fixes...
if file[-5:] == ".info":
file_contents = file_contents.replace("organism="+org,"organism="+builds[org]['build'])
file_contents = file_contents.replace("refseq="+builds[org]['chrs'][chrom],"refseq="+chrom)
#write out new file
file_out = open(new_name,'w')
file_out.write(file_contents)
file_out.close()
#write out org info file and remove old file
org_info_out = open(info_file_new,'w')
org_info_out.write(info_file_contents)
org_info_out.close()
os.unlink(info_file_old)
#change org directory name
move(old_dir,new_dir)