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This commit is contained in:
greg
2022-11-21 09:18:36 -05:00
parent fd2d4083eb
commit fa410aa2d6
2 changed files with 18 additions and 68 deletions
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lib/galaxy/datatypes/registry.py
-3
View File
@@ -711,7 +711,6 @@ class Registry:
"customtrack": interval.CustomTrack(),
"csfasta": sequence.csFasta(),
"fasta": sequence.Fasta(),
"psl": tabular.Psl(),
"eland": tabular.Eland(),
"fastq": sequence.Fastq(),
"fastqsanger": sequence.FastqSanger(),
@@ -760,7 +759,6 @@ class Registry:
"maf": "text/plain",
"memexml": "application/xml",
"pileup": "text/plain",
"psl": "text/plain",
"qualsolid": "text/plain",
"qualsolexa": "text/plain",
"qual454": "text/plain",
@@ -805,7 +803,6 @@ class Registry:
interval.Gff(),
interval.Gff3(),
tabular.Pileup(),
tabular.Psl(),
interval.Interval(),
tabular.Sam(),
tabular.Eland(),
lib/galaxy/datatypes/tabular.py
+18 -65
View File
@@ -1817,10 +1817,6 @@ class Psl(Tabular):
"tStarts",
]
def display_peek(self, dataset):
"""Returns formated html of peek"""
return self.make_html_table(dataset, column_names=self.column_names)
def sniff_prefix(self, file_prefix: FilePrefix):
"""
PSL lines represent alignments, and are typically generated
@@ -1862,6 +1858,11 @@ class Psl(Tabular):
>>> Psl().sniff( fname )
False
"""
def check_items(s):
s_items = s.split(",")
for item in s_items:
if int(item) < 0:
raise Exception("Out of range")
count = 0
for line in file_prefix.line_iterator():
line = line.strip()
@@ -1874,72 +1875,24 @@ class Psl(Tabular):
items = line.split("\t")
if len(items) != 21:
return False
# matches
if int(items[0]) < 0:
raise Exception("Out of range")
# misMatches
if int(items[1]) < 0:
raise Exception("Out of range")
# repMatches
if int(items[2]) < 0:
raise Exception("Out of range")
# nCount
if int(items[3]) < 0:
raise Exception("Out of range")
# qNumInsert
if int(items[4]) < 0:
raise Exception("Out of range")
# qBaseInsert
if int(items[5]) < 0:
raise Exception("Out of range")
# tNumInsert
if int(items[6]) < 0:
raise Exception("Out of range")
# tBaseInsert
if int(items[7]) < 0:
raise Exception("Out of range")
# tName is a string
items.pop(13)
# qName is a string
items.pop(9)
# strand
if items[8] not in ["-", "+", "+-", "-+"]:
if items.pop(8) not in ["-", "+", "+-", "-+"]:
raise Exception("Invalid strand")
# qSize
if int(items[10]) < 0:
raise Exception("Out of range")
# qStart
if int(items[11]) < 0:
raise Exception("Out of range")
# qEnd
if int(items[12]) < 0:
raise Exception("Out of range")
# tSize
if int(items[14]) < 0:
raise Exception("Out of range")
# tStart
if int(items[15]) < 0:
raise Exception("Out of range")
# tEnd
if int(items[16]) < 0:
raise Exception("Out of range")
# blockCount
if int(items[17]) < 0:
raise Exception("Out of range")
# blockSizes
s = items[18].rstrip(",")
s_items = s.split(",")
for item in s_items:
if int(item) < 0:
raise Exception("Out of range")
s = items.pop(15).rstrip(",")
check_items(s)
# qStarts
s = items[19].rstrip(",")
s_items = s.split(",")
for item in s_items:
if int(item) < 0:
raise Exception("Out of range")
s = items.pop(15).rstrip(",")
check_items(s)
# tStarts
s = items[20].rstrip(",")
s_items = s.split(",")
for item in s_items:
if int(item) < 0:
raise Exception("Out of range")
s = items.pop(15).rstrip(",")
check_items(s)
if any(int(item) < 0 for item in items):
raise Exception("Out of range")
count += 1
if count == 10:
break