Building a Glycan Hypothesis from a Text File¶

When a comprehensive list of glycan compositions is available, you can translate them into a list encoded in IUPAClite with one composition per line. Lines may have the form

<composition>  [<classifier>[  <classifier>...]]
<composition>  [<classifier>[  <classifier>...]]
...

where classifier is one of the recognized glycan composition classifiers such as N-glycan, O-glycan, or GAG-linker. For more information on glycan composition classifiers, please see Glycan Composition Classes.

glycresoft build-hypothesis glycan-text¶

glycresoft build-hypothesis glycan-text [OPTIONS] TEXT_FILE
                                        DATABASE_CONNECTION

Options

-r, --reduction <string>¶: Reducing end modification

-d, --derivatization <string>¶: Chemical derivatization to apply

-n, --name <string>¶: The name for the hypothesis to be created

Arguments

TEXT_FILE¶: Required argument <path>

DATABASE_CONNECTION¶: Required argument <string> A connection URI for a database, or a path on the file system

For more information on reductions and derivatizations, please see Glycan Modifications

Usage Example¶

$ head glycan-compositions.txt
{Hex:5; HexNAc:4; Neu5Ac:1}  N-Glycan
{Hex:5; HexNAc:4; Neu5Ac:2}  N-Glycan
{Fuc:1; Hex:5; HexNAc:4; Neu5Ac:2}  N-Glycan
{Fuc:2; Hex:6; HexNAc:5; Neu5Ac:1}  N-Glycan
{Fuc:1; Hex:6; HexNAc:5; Neu5Ac:2}  N-Glycan

$ wc -l glycan-compositions.txt
41 glycan-compositions.txt

$ glycresoft build-hypothesis glycan-text glycan-compositions.txt glycan-list.db -n "N-Glycan short list"
Building Glycan Hypothesis N-Glycan short list
13:51:54 - glycresoft:log:175 - INFO - Begin Text File Glycan Hypothesis Serializer
{'derivatization': None,
 'engine': Engine(sqlite:///glycan-list.db),
 'glycan_file': u'glycan-compositions.txt',
 'loader': None,
 'reduction': None,
 'start_time': datetime.datetime(2017, 8, 31, 13, 51, 54, 636000),
 'status': 'started',
 'transformer': None,
 'uuid': '10e06326097c41f4beeeddd8e17bbc0e'}
13:51:54 - glycresoft:log:175 - INFO - Loading Glycan Compositions from Stream for GlycanHypothesis(id=1, name=N-Glycan short list)
13:51:54 - glycresoft:log:175 - INFO - Generated 41 glycan compositions
13:51:54 - glycresoft:log:175 - INFO - Hypothesis Completed
13:51:54 - glycresoft:log:175 - INFO - End Text File Glycan Hypothesis Serializer
13:51:54 - glycresoft:log:175 - INFO - Started at 2017-08-31 13:51:54.636000.
Ended at 2017-08-31 13:51:54.761000.
Total time elapsed: 0:00:00.125000
TextFileGlycanHypothesisSerializer completed successfully.