opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-21 13:50:20 +08:00
Code Issues Packages Projects Releases Wiki Activity

Much better approach to determining datatype in order to ensure columns and column_list metadata attributes are properly set.

Browse Source
This commit is contained in:
Greg Von Kuster
2007-09-08 15:53:15 +00:00
parent 9235051818
commit dd64d676b1
1 changed files with 51 additions and 19 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/datatypes/tabular.py
+51 -19
View File
@@ -41,28 +41,63 @@ class Tabular( data.Text ):
if dataset.has_data():
column_types = []
format = sniff.guess_ext( dataset.file_name )
if dataset.extension != format:
"""
We need to rely on the ability of our sniffer to properly detect datatypes here since
there are many ways that the datatype could be improperly set.
TODO: we may want to automatically convert the datset to the proper datatype here,
but for now we'll leave it and just rely on the value in format.
"""
pass
"""
The 'proceed' value allows us to skip different numbers of lines based on the data
format (type). We need this because different formats can include lines of information
that are not properly commented (properly commented lines start with a '#' character).
"""
"""
proceed = False
col1_startswith = ['chr', 'chl', 'groupun', 'reftig_', 'scaffold', 'super_', 'vcho']
for i, line in enumerate( file ( dataset.file_name ) ):
"""
This seems kind of hacky, but many times an input file will have
an invalid comment on the first line (a comment without a # character
to start), so we'll always skip the first line.
"""
if proceed:
line = line.rstrip('\r\n')
valid = True
if line and not line.startswith( '#' ):
elems = line.split( '\t' )
elems_len = len(elems)
if elems_len > 0:
line = line.rstrip('\r\n')
valid = True
if line and not line.startswith( '#' ):
elems = line.split( '\t' )
elems_len = len(elems)
if elems_len > 0:
if format == 'bed':
for str in col1_startswith:
if elems[0].lower().startswith(str):
proceed = True
break
elif forrmat == 'interval':
if elems_len > 2:
try:
map( int, [elems[1], elems[2]] )
proceed = True
except:
pass # proceed is False
elif format == 'gff':
if elems_len == 9:
try:
map( int, [hdr[3], hdr[4]] )
proceed = True
except:
pass
elif format=='wig':
try:
int( elems[0] )
proceed = True
except:
for str in col1_startswith:
if elems[0].lower().startswith(str):
proceed = True
break
elif format =='tabular' and i > 1:
proceed = True
if proceed:
"""Set the columns metadata attribute"""
if elems_len != dataset.metadata.columns:
dataset.metadata.columns = elems_len
@@ -97,10 +132,7 @@ class Tabular( data.Text ):
column_types.append(col_type)
if len(column_types) > 0: break
elif ( format=='tabular' or format=='interval' or format=='bed' or format=='gff') and i > 1:
proceed = True
elif format=='wig' and i > 30:
proceed = True
if i > 100: break # Hopefully we never get here...
dataset.metadata.column_types = column_types