diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py index ffa11e25a2f..28fbe4754be 100644 --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -694,13 +694,16 @@ class BaseFastq(Sequence): >>> fname = get_test_fname('1.fastqsanger') >>> FastqSanger().sniff(fname) True + >>> fname = get_test_fname('4.fastqsanger') + >>> FastqSanger().sniff(fname) + True >>> fname = get_test_fname('3.fastq') >>> FastqSanger().sniff(fname) False >>> Fastq().sniff(fname) True >>> fname = get_test_fname('2.fastq') - >>> Fastq().sniff( fname ) + >>> Fastq().sniff(fname) True >>> FastqSanger().sniff(fname) False @@ -819,7 +822,7 @@ class FastqSanger(Fastq): def quality_check(lines): """Presuming lines are lines from a fastq file, return True if the qualities are compatible with sanger encoding""" for line in islice(lines, 3, None, 4): - if not all(_ >= '!' and _ <= 'M' for _ in line[0]) or ' ' in line: + if not all(_ >= '!' and _ <= 'S' for _ in line[0]): return False return True diff --git a/lib/galaxy/datatypes/test/4.fastqsanger b/lib/galaxy/datatypes/test/4.fastqsanger new file mode 100644 index 00000000000..ff60d92d068 --- /dev/null +++ b/lib/galaxy/datatypes/test/4.fastqsanger @@ -0,0 +1,8 @@ +@DCW97JN1:309:C0C42ACXX:4:2206:12976:57510/1 +AAATGGGCATAATATAGATGTAGAGATGTGTTGAATTTATGACTCATTT ++ +ADECJJJJDCCECCCCMCCNCCMCNBCLBJBCLADCDC=CNDJILEDDD +@DCW97JN1:309:C0C42ACXX:4:2211:6915:3569/1 +AAAGAAATTAAATGGGCATAATATAGATGTAGAGATGTGTTGAATTTAT ++ +@DEJAAA?B@ECCEFFGDBBFC8ABGCBK=BI=66@HE@@JACCCDCCI