| Previous changeset 2:b65518a007fa (2013-09-08) Next changeset 4:7c1f9962ac07 (2013-09-27) |
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Commit message:
Uploaded |
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modified:
get_pubchem/get_pubchem_as_smiles.py get_pubchem/get_pubchem_as_smiles.xml |
| b |
| diff -r b65518a007fa -r 021f0ef9474f get_pubchem/get_pubchem_as_smiles.py --- a/get_pubchem/get_pubchem_as_smiles.py Sun Sep 08 09:42:57 2013 -0400 +++ b/get_pubchem/get_pubchem_as_smiles.py Wed Sep 18 09:44:36 2013 -0400 |
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| @@ -29,7 +29,7 @@ result.get() for filename in os.listdir(td): - path = os.path.join(td, filename) + path = os.path.join(td, filename) + '.smi' shutil.copyfileobj(open(path, 'rb'), output_handle) output_handle.close() @@ -38,9 +38,9 @@ def fetch_convert(args): (filename, td) = args - tmp_name = os.path.join( tempfile.gettempdir(), filename) + tmp_name = os.path.join( td, filename) subprocess.call( ['wget', '-O', tmp_name, os.path.join('ftp://ftp.ncbi.nih.gov/pubchem/Compound/CURRENT-Full/SDF/', filename)] ) - output = os.path.join(td, filename) + output = os.path.join(td, filename) + '.smi' subprocess.call(["obabel", "-isdf", tmp_name, "-ocan", '-O', output]) os.remove(tmp_name) |
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| diff -r b65518a007fa -r 021f0ef9474f get_pubchem/get_pubchem_as_smiles.xml --- a/get_pubchem/get_pubchem_as_smiles.xml Sun Sep 08 09:42:57 2013 -0400 +++ b/get_pubchem/get_pubchem_as_smiles.xml Wed Sep 18 09:44:36 2013 -0400 |
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| @@ -1,23 +1,36 @@ <tool id="ctb_pubchem_download_as_smiles" name="PubChem Download" Version="0.1" > - <description>as canonical SMILES</description> - <requirements> - <requirement type="package" version="2.3.2">openbabel</requirement> - </requirements> - <command interpreter="python"> + <description>as canonical SMILES</description> + <requirements> + <requirement type="package" version="2.3.2">openbabel</requirement> + </requirements> + <command interpreter="python"> get_pubchem_as_smiles.py -o $pubchem_smi -p 4 - 2>&1 - </command> - <inputs> - <param name="infile" type="select" display="radio" size="250" label="Load all pubchem files and convert them to canonical smiles." /> - </inputs> - <outputs> - <data format="smi" name="pubchem_smi" /> - </outputs> - <tests> - </tests> - <help> + </command> + <stdio> + <regex match="obError" + source="both" + level="fatal" + description="Critical Open Babel error" /> + <regex match="obWarning" + source="both" + level="warning" + description="Non-critical Open Babel warning" /> + <regex match="obInfo" + source="both" + level="log" + description="Open Babel Information" /> + </stdio> + <inputs> + <param name="infile" type="select" display="radio" size="250" label="Load all pubchem files and convert them to canonical smiles." /> + </inputs> + <outputs> + <data format="smi" name="pubchem_smi" /> + </outputs> + <tests> + </tests> + <help> .. class:: infomark @@ -35,5 +48,5 @@ The output will be one large SMILES file. - </help> + </help> </tool> |