Mercurial > repos > galaxyp > peptideshaker

annotate admin_scripts/build_mods_loc.py @ 32:ff592231f118 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
author galaxyp
date Wed, 25 Jan 2017 15:37:43 -0500
parents 2cafc729b2ae
children bb0130ff73ce
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
1 #!/usr/bin/env python
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
2
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
3 import xml.etree.ElementTree as ET
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
4 from os.path import exists
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
5
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
6 with open("searchgui_mods.loc.sample", "w") as output:
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
7 for mods_path in ["searchGUI_mods.xml", "searchGUI_usermods.xml"]:
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
8 tree = ET.parse(mods_path)
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
9 modifications_el = tree.getroot()
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
10 for mod in modifications_el.findall("{http://www.ncbi.nlm.nih.gov}MSModSpec"):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
11 name_el = mod.find("{http://www.ncbi.nlm.nih.gov}MSModSpec_name")
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
12 output.write("%s\n" % name_el.text.lower())