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Merge pull request #4239 from dpryan79/sniffSkipComments

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Enable skipping comment lines while sniffing files
This commit is contained in:
Nicola Soranzo
2017-06-28 08:15:03 +02:00
committed by GitHub
parent 6cd026bc7b e5e83833d1
commit 40cd2df06b
2 changed files with 17 additions and 7 deletions
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lib/galaxy/datatypes/interval.py
+4 -4
View File
@@ -314,14 +314,14 @@ class Interval( Tabular ):
>>> Interval().sniff( fname )
True
"""
headers = get_headers( filename, '\t' )
headers = get_headers( filename, '\t', comment_designator='#' )
try:
"""
If we got here, we already know the file is_column_based and is not bed,
so we'll just look for some valid data.
"""
for hdr in headers:
if hdr and not hdr[0].startswith( '#' ):
if hdr:
if len(hdr) < 3:
return False
try:
@@ -504,12 +504,12 @@ class Bed( Interval ):
>>> Bed().sniff( fname )
True
"""
headers = get_headers( filename, '\t' )
headers = get_headers( filename, '\t', comment_designator='#' )
try:
if not headers:
return False
for hdr in headers:
if (hdr[0] == '' or hdr[0].startswith( '#' )):
if hdr[0] == '':
continue
valid_col1 = False
if len(hdr) < 3 or len(hdr) > 12:
lib/galaxy/datatypes/sniff.py
+13 -3
View File
@@ -198,24 +198,34 @@ def convert_newlines_sep2tabs( fname, in_place=True, patt="\\s+", tmp_dir=None,
return ( i + 1, temp_name )
def get_headers( fname, sep, count=60, is_multi_byte=False ):
def get_headers( fname, sep, count=60, is_multi_byte=False, comment_designator=None ):
"""
Returns a list with the first 'count' lines split by 'sep'
Returns a list with the first 'count' lines split by 'sep', ignoring lines
starting with 'comment_designator'
>>> fname = get_test_fname('complete.bed')
>>> get_headers(fname,'\\t')
[['chr7', '127475281', '127491632', 'NM_000230', '0', '+', '127486022', '127488767', '0', '3', '29,172,3225,', '0,10713,13126,'], ['chr7', '127486011', '127488900', 'D49487', '0', '+', '127486022', '127488767', '0', '2', '155,490,', '0,2399']]
>>> fname = get_test_fname('test.gff')
>>> get_headers(fname, '\\t', count=5, comment_designator='#')
[[''], ['chr7', 'bed2gff', 'AR', '26731313', '26731437', '.', '+', '.', 'score'], ['chr7', 'bed2gff', 'AR', '26731491', '26731536', '.', '+', '.', 'score'], ['chr7', 'bed2gff', 'AR', '26731541', '26731649', '.', '+', '.', 'score'], ['chr7', 'bed2gff', 'AR', '26731659', '26731841', '.', '+', '.', 'score']]
"""
headers = []
in_file = compression_utils.get_fileobj(fname)
try:
for idx, line in enumerate(in_file):
idx = 0
for line in in_file:
line = line.rstrip('\n\r')
if is_multi_byte:
# TODO: fix this - sep is never found in line
line = unicodify( line, 'utf-8' )
sep = sep.encode( 'utf-8' )
if comment_designator is not None and comment_designator != '':
comment_designator = comment_designator.encode( 'utf-8' )
if comment_designator is not None and comment_designator != '' and line.startswith( comment_designator ):
continue
headers.append( line.split(sep) )
idx += 1
if idx == count:
break
finally: