Commits · 4dda3c4781f5e9911911eba0623a55bbcbe327c4 · SOaAS / psot.repository

13 Dec, 2017 2 commits
- 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
12 Dec, 2017 5 commits
- Merge branch 'fix-include-sequence' into 'develop' · 5e73cabf
  Lukas Jelonek authored Dec 12, 2017
```
Fix loss of last fasta entry. Solves #31

See merge request SOaAS/psot!7
```
  5e73cabf
- Merge branch 'tmhmm' into 'develop' · 639c784e
  Lukas Jelonek authored Dec 12, 2017
```
Tmhmm

See merge request SOaAS/psot!5
```
  639c784e
- merge develop into tmhmm · c1d124d9
  lmueller authored Dec 12, 2017
  
  c1d124d9
- added resolve_dbxrefs.py to nextflow.py (not working yet) · 458a3c11
  lmueller authored Dec 12, 2017
  
  458a3c11
- Merge branch 'fasta-header-decomplexify' into 'develop' · 5a3cc5ad
  Lukas Jelonek authored Dec 12, 2017
```
Fasta header decomplexify

See merge request SOaAS/psot!6
```
  5a3cc5ad
11 Dec, 2017 1 commit
- added taxonomy dbxrefs to testfile · 57eb76c6
  lmueller authored Dec 11, 2017
  
  57eb76c6
08 Dec, 2017 1 commit
- Fix loss of last fasta entry. Solves #31 · 171d47d8
  hmueller authored Dec 08, 2017
  
  171d47d8
07 Dec, 2017 8 commits
- bundle dbxrefs before retrieving them => fewer calls · f2096889
  lmueller authored Dec 07, 2017
  
  f2096889
- Define enumerated header filename in run scripts and pass it to header... · ad087cc8
  hmueller authored Dec 07, 2017
```
Define enumerated header filename in run scripts and pass it to header enumeration script instead of passing result directory.
```
  ad087cc8
- Minor improvements in code readability. · 610ed0d9
  hmueller authored Dec 07, 2017
  
  610ed0d9
- Add targetp to list of required tools. · 88914353
  hmueller authored Dec 07, 2017
  
  88914353
- Include fasta header conversion and restoration steps in targetp module scripts. · 61c16030
  hmueller authored Dec 07, 2017
  
  61c16030
- adapted resolve_dbxrefs.py to input format · c0db9a40
  lmueller authored Dec 07, 2017
  
  c0db9a40
- Remove redundant sequence id field from results section of targetp in json output. · a2f733d3
  hmueller authored Dec 07, 2017
  
  a2f733d3
- Pass directory instead of file between targetp run and convert processes. · 7b15f5e7
  hmueller authored Dec 07, 2017
  
  7b15f5e7
06 Dec, 2017 2 commits
- Minor code cleanup. · 6ddf8881
  hmueller authored Dec 06, 2017
  
  6ddf8881
- Include fasta header conversion and restoration steps in ghostx module scripts. · 6f1bf564
  hmueller authored Dec 06, 2017
  
  6f1bf564
05 Dec, 2017 5 commits
- Add script to restore original seq ids in json results file from enumeration. · 05fd6a68
  hmueller authored Dec 05, 2017
  
  05fd6a68
- Change filename and manipulate file in place instead of creating a new one. · 045ac89e
  hmueller authored Dec 05, 2017
  
  045ac89e
- Merge branch 'hmmscan-empty-results' into 'develop' · ebb26a4a
  Lukas Jelonek authored Dec 05, 2017
```
Hmmscan empty results

See merge request SOaAS/psot!4
```
  ebb26a4a
- Add script for exchange of fasta headers with enumeration. · 42345e6a
  hmueller authored Dec 05, 2017
  
  42345e6a
- added not working dbxrefs to test file · 9d4265ae
  lmueller authored Dec 05, 2017
  
  9d4265ae
04 Dec, 2017 3 commits
- use retrieve function in dbxref retriever.py instead of calling every retriever skript separately · e4a26419
  lmueller authored Dec 04, 2017
  
  e4a26419
- Make sequence ID extraction from fasta header more robust so that it works... · f404a49c
  hmueller authored Dec 04, 2017
```
Make sequence ID extraction from fasta header more robust so that it works with more complex headers, too.
```
  f404a49c
- Replace string with empty list to indicate no matches. · 22f5b240
  hmueller authored Dec 04, 2017
  
  22f5b240
01 Dec, 2017 3 commits
- Minor code cosmetics · c6f18289
  hmueller authored Dec 01, 2017
  
  c6f18289
- Write "no match found" for results list when query had no matches. · 1e084c41
  hmueller authored Dec 01, 2017
  
  1e084c41
- Implement simple storage of query sequence names. Currently relies on resolution of issue #22. · 6a80c032
  hmueller authored Dec 01, 2017
  
  6a80c032
30 Nov, 2017 9 commits
- Merge branch 'targetp' into 'develop' · f67b0373
  Lukas Jelonek authored Nov 30, 2017
```
Targetp

See merge request SOaAS/psot!1
```
  f67b0373
- Merge branch 'develop' into targetp · 6c59cd12
  Lukas Jelonek authored Nov 30, 2017
  
  6c59cd12
- 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
- Merge commit '9db2c064 ' into develop · c040c5fd
  Lukas Jelonek authored Nov 30, 2017
  
  c040c5fd
- 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
29 Nov, 2017 1 commit
- got resolve_dbxrefs.py working, still unstable · 5ea07f52
  lmueller authored Nov 29, 2017
  
  5ea07f52