Mercurial > repos > jjohnson > peptideshaker

annotate admin_scripts/build_mods_loc.py @ 0:8b99cb00e1c4 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 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
author jjohnson
date Tue, 15 May 2018 14:50:35 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
1 #!/usr/bin/env python
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
2
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
3 import xml.etree.ElementTree as ET
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
4 from os.path import exists
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
5
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
6 with open("searchgui_mods.loc.sample", "w") as output:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
7 for mods_path in ["searchGUI_mods.xml", "searchGUI_usermods.xml"]:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
8 tree = ET.parse(mods_path)
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
9 modifications_el = tree.getroot()
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
10 for mod in modifications_el.findall("{http://www.ncbi.nlm.nih.gov}MSModSpec"):
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
11 name_el = mod.find("{http://www.ncbi.nlm.nih.gov}MSModSpec_name")
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
12 output.write("%s\n" % name_el.text.lower())