Commits · 4dda3c4781f5e9911911eba0623a55bbcbe327c4 · SOaAS / psot.repository · GitLab

Snippets Groups Projects

Dec 13, 2017
- Include mature sequence in json output if available. · 4dda3c47
  hmueller authored Dec 13, 2017
  
  4dda3c47
- Make signalp run script accept optional include_mature flag. · f72da30b
  hmueller authored Dec 13, 2017
  
  f72da30b
Dec 12, 2017
- added resolve_dbxrefs.py to nextflow.py (not working yet) · 458a3c11
  lmueller authored Dec 12, 2017
  
  458a3c11
Dec 08, 2017
- Fix loss of last fasta entry. Solves #31 · 171d47d8
  hmueller authored Dec 8, 2017
  
  171d47d8
Dec 07, 2017
- bundle dbxrefs before retrieving them => fewer calls · f2096889
  lmueller authored Dec 7, 2017
  
  f2096889
- Define enumerated header filename in run scripts and pass it to header... · ad087cc8
  hmueller authored Dec 7, 2017
  ad087cc8
- Minor improvements in code readability. · 610ed0d9
  hmueller authored Dec 7, 2017
  
  610ed0d9
- Include fasta header conversion and restoration steps in targetp module scripts. · 61c16030
  hmueller authored Dec 7, 2017
  
  61c16030
- adapted resolve_dbxrefs.py to input format · c0db9a40
  lmueller authored Dec 7, 2017
  
  c0db9a40
- Remove redundant sequence id field from results section of targetp in json output. · a2f733d3
  hmueller authored Dec 7, 2017
  
  a2f733d3
- Pass directory instead of file between targetp run and convert processes. · 7b15f5e7
  hmueller authored Dec 7, 2017
  
  7b15f5e7
Dec 06, 2017
- Minor code cleanup. · 6ddf8881
  hmueller authored Dec 6, 2017
  
  6ddf8881
- Include fasta header conversion and restoration steps in ghostx module scripts. · 6f1bf564
  hmueller authored Dec 6, 2017
  
  6f1bf564
Dec 05, 2017
- Add script to restore original seq ids in json results file from enumeration. · 05fd6a68
  hmueller authored Dec 5, 2017
  
  05fd6a68
- Change filename and manipulate file in place instead of creating a new one. · 045ac89e
  hmueller authored Dec 5, 2017
  
  045ac89e
- Add script for exchange of fasta headers with enumeration. · 42345e6a
  hmueller authored Dec 5, 2017
  
  42345e6a
Dec 04, 2017
- use retrieve function in dbxref retriever.py instead of calling every retriever skript separately · e4a26419
  lmueller authored Dec 4, 2017
  
  e4a26419
- Make sequence ID extraction from fasta header more robust so that it works... · f404a49c
  hmueller authored Dec 4, 2017
  f404a49c
- Replace string with empty list to indicate no matches. · 22f5b240
  hmueller authored Dec 4, 2017
  
  22f5b240
Dec 01, 2017
- Minor code cosmetics · c6f18289
  hmueller authored Dec 1, 2017
  
  c6f18289
- Write "no match found" for results list when query had no matches. · 1e084c41
  hmueller authored Dec 1, 2017
  
  1e084c41
- Implement simple storage of query sequence names. Currently relies on resolution of issue #22. · 6a80c032
  hmueller authored Dec 1, 2017
  
  6a80c032
Nov 30, 2017
- Cleanup code · 8dbbeca4
  Lukas Jelonek authored Nov 30, 2017
  
  8dbbeca4
- fixed tmhmm json format · ec72c85d
  lmueller authored Nov 30, 2017 and Lukas Jelonek committed Nov 30, 2017
  
  ec72c85d
- Translate location identifiers into more verbose representations. · 6a22244c
  hmueller authored Nov 30, 2017
  
  6a22244c
- fixed tmhmm json format · e9e5fe63
  lmueller authored Nov 30, 2017
  
  e9e5fe63
- Reduce code redundancy. · 1c531d81
  hmueller authored Nov 30, 2017
  
  1c531d81
- fixed pfam bug in resolve_dbxrefs.py · bf196bb1
  lmueller authored Nov 30, 2017
  
  bf196bb1
Nov 29, 2017
- got resolve_dbxrefs.py working, still unstable · 5ea07f52
  lmueller authored Nov 29, 2017
  
  5ea07f52
Nov 28, 2017
- Use string type organism_mode instead of boolean plantmode parameter. · df258571
  hmueller authored Nov 28, 2017
  
  df258571
- Change organism type parameter from boolean to string type. · e2a4af22
  hmueller authored Nov 28, 2017
  
  e2a4af22
- Add TargetP to json converter. · 29590252
  hmueller authored Nov 28, 2017
  
  29590252
Nov 27, 2017
- Add run_targetp.py script. · 193e2cef
  hmueller authored Nov 27, 2017
  
  193e2cef
Nov 16, 2017
- created resolve_dbxrefs.py (not working yet) and according testfiles · 89c7cfc7
  lmueller authored Nov 16, 2017
  
  89c7cfc7
Nov 09, 2017
- fixed bug in topology-string resolver · e17691d6
  lmueller authored Nov 9, 2017
  
  e17691d6
Nov 08, 2017
- added method to resolve topology-string from tmhmm output · f08f7db6
  lmueller authored Nov 8, 2017
  
  f08f7db6
Oct 18, 2017
- added tmhmm module · 202ab9c1
  lmueller authored Oct 18, 2017
  
  202ab9c1
Aug 07, 2017
- Removed threads from blast runner · 8487d7da
  Lukas Jelonek authored Aug 7, 2017
  
  8487d7da
- Fix bug: ghostx adds the whole fasta header as a query to its results · 395eb134
  Lukas Jelonek authored Aug 7, 2017
  
  395eb134
Aug 02, 2017
- Use env import instead of changing the module search path by hand in run scripts · 4be6ffd5
  Lukas Jelonek authored Aug 2, 2017
  
  4be6ffd5