[galaxy-dev] [hg] galaxy 3459: Change color space FASTA file type from fastqs...

details: http://www.bx.psu.edu/hg/galaxy/rev/8bd2ace6c92d changeset: 3459:8bd2ace6c92d user: Dan Blankenberg <dan@bx.psu.edu> date: Tue Mar 02 10:47:23 2010 -0500 description: Change color space FASTA file type from fastqsolid to fastqcssanger. Cripple accepted tool input formats for many of the FASTQ tools to only allow only fastqsanger and fastqcssanger to be used. diffstat: datatypes_conf.xml.sample | 2 +- lib/galaxy/datatypes/sequence.py | 6 +- lib/galaxy_utils/sequence/fasta.py | 2 +- lib/galaxy_utils/sequence/fastq.py | 6 +- test-data/combine_phiX_out_1.fastqcssanger | 576 +++++++++++++ test-data/combine_phiX_out_1.fastqsolid | 576 ------------- test-data/combine_phiX_out_2.fastqcssanger | 576 +++++++++++++ test-data/combine_phiX_out_2.fastqsolid | 576 ------------- test-data/fastq_combiner_no_qual_ascii_out_1.fastqcssanger | 576 +++++++++++++ test-data/fastq_combiner_no_qual_ascii_out_1.fastqsolid | 576 ------------- test-data/illumina_full_range_as_cssanger.fastqcssanger | 8 + test-data/illumina_full_range_as_solid.fastqsolid | 8 - test-data/sanger_full_range_as_cssanger.fastqcssanger | 8 + test-data/sanger_full_range_as_solid.fastqsolid | 8 - test-data/solexa_full_range_as_cssanger.fastqcssanger | 8 + test-data/solexa_full_range_as_solid.fastqsolid | 8 - tool_conf.xml.sample | 19 +- tools/fastq/fastq_combiner.py | 2 +- tools/fastq/fastq_combiner.xml | 15 +- tools/fastq/fastq_filter.xml | 32 +- tools/fastq/fastq_groomer.xml | 50 +- tools/fastq/fastq_manipulation.xml | 19 +- tools/fastq/fastq_paired_end_joiner.xml | 4 +- tools/fastq/fastq_paired_end_splitter.xml | 2 +- tools/fastq/fastq_stats.xml | 12 +- tools/fastq/fastq_to_fasta.xml | 2 +- tools/fastq/fastq_trimmer.xml | 12 +- 27 files changed, 1848 insertions(+), 1841 deletions(-) diffs (truncated from 4157 to 3000 lines): diff -r 19d8ba4269ba -r 8bd2ace6c92d datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Tue Mar 02 09:51:05 2010 -0500 +++ b/datatypes_conf.xml.sample Tue Mar 02 10:47:23 2010 -0500 @@ -35,7 +35,7 @@ <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true"/> <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"/> <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true"/> - <datatype extension="fastqsolid" type="galaxy.datatypes.sequence:FastqSolid" display_in_upload="true"/> + <datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true"/> <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true"/> <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"> <!-- <display file="genetrack.xml" /> --> diff -r 19d8ba4269ba -r 8bd2ace6c92d lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Tue Mar 02 09:51:05 2010 -0500 +++ b/lib/galaxy/datatypes/sequence.py Tue Mar 02 10:47:23 2010 -0500 @@ -224,9 +224,9 @@ """Class representing a FASTQ sequence ( the Illumina 1.3+ variant )""" file_ext = "fastqillumina" -class FastqSolid( Fastq ): - """Class representing a FASTQ sequence ( the SOLiD (color space) variant )""" - file_ext = "fastqsolid" +class FastqCSSanger( Fastq ): + """Class representing a Color Space FASTQ sequence ( e.g a SOLiD variant )""" + file_ext = "fastqcssanger" try: from galaxy import eggs diff -r 19d8ba4269ba -r 8bd2ace6c92d lib/galaxy_utils/sequence/fasta.py --- a/lib/galaxy_utils/sequence/fasta.py Tue Mar 02 09:51:05 2010 -0500 +++ b/lib/galaxy_utils/sequence/fasta.py Tue Mar 02 10:47:23 2010 -0500 @@ -104,7 +104,7 @@ def __init__( self, fh ): self.file = fh def write( self, fastq_read ): - #this will include SOLiD adapter base if applicable + #this will include color space adapter base if applicable self.file.write( ">%s\n%s\n" % ( fastq_read.identifier[1:], fastq_read.sequence ) ) def close( self ): return self.file.close() diff -r 19d8ba4269ba -r 8bd2ace6c92d lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py Tue Mar 02 09:51:05 2010 -0500 +++ b/lib/galaxy_utils/sequence/fastq.py Tue Mar 02 10:47:23 2010 -0500 @@ -176,8 +176,8 @@ score_system = 'solexa' sequence_space = 'base' -class fastqSolidRead( fastqSequencingRead ): - format = 'solid' #color space +class fastqCSSangerRead( fastqSequencingRead ): + format = 'cssanger' #color space ascii_min = 33 ascii_max = 126 quality_min = 0 @@ -260,7 +260,7 @@ FASTQ_FORMATS = {} -for format in [ fastqIlluminaRead, fastqSolexaRead, fastqSangerRead, fastqSolidRead ]: +for format in [ fastqIlluminaRead, fastqSolexaRead, fastqSangerRead, fastqCSSangerRead ]: FASTQ_FORMATS[ format.format ] = format diff -r 19d8ba4269ba -r 8bd2ace6c92d test-data/combine_phiX_out_1.fastqcssanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combine_phiX_out_1.fastqcssanger Tue Mar 02 10:47:23 2010 -0500 @@ -0,0 +1,576 @@ +@1831_573_1004_F3 +T00030133312212111300011021310132222 ++ +4 29 27 34 5 5 24 24 20 17 10 34 29 20 27 13 30 27 22 24 11 28 19 17 27 17 24 17 25 27 7 24 14 12 22 +@1831_573_1050_F3 +T03330322230322112131010221102122113 ++ +8 26 31 31 16 22 30 31 28 29 22 30 30 31 32 23 30 28 28 31 19 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-@1831_577_692_F3 -T01122320200330103121202301211100220 -+ -@B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< diff -r 19d8ba4269ba -r 8bd2ace6c92d test-data/fastq_combiner_no_qual_ascii_out_1.fastqcssanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_combiner_no_qual_ascii_out_1.fastqcssanger Tue Mar 02 10:47:23 2010 -0500 @@ -0,0 +1,576 @@ +@1831_573_1004_F3 +T00030133312212111300011021310132222 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_573_1050_F3 +T03330322230322112131010221102122113 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_573_1067_F3 +T00023032023103330112220321200200002 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_573_1219_F3 +T11211130300300301021212330201121310 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_573_1242_F3 +T02132003121011302100130302112221121 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_573_1333_F3 +T00200312330110101013212313222303112 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_573_1362_F3 +T21203131001102231121211101111321131 ++ 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++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_266_F3 +T30322223101312011300311121221333223 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_327_F3 +T22112331301313021321001332120332130 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_331_F3 +T32012133301311223023011232112333030 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_387_F3 +T00101211032031120300200222001230022 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_406_F3 +T00223133010210122221320212103132011 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_449_F3 +T31312001121222231100020132132100220 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_519_F3 +T03011321130130133213131202130321131 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_603_F3 +T21003032313302312320131221001330311 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_655_F3 +T02001023130302322122200313123123102 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_677_F3 +T13330131023320301031013230210103022 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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+T00332022110020300332022020202002232 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_281_F3 +T03032301231212301013112222111210000 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_288_F3 +T01031120221303100221230021013201130 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_322_F3 +T12003213220230103303201000130312202 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_362_F3 +T31203302330110131230331210121110220 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_382_F3 +T32312123033111120321303230201332100 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_464_F3 +T13020221011130013102221333131203302 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_488_F3 +T13200302330322110200323132101120301 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_511_F3 +T32232133031023313331312220133230333 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_545_F3 +T00112131333222303222210031322103233 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_559_F3 +T32321101303233120102011130022122002 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_562_F3 +T32331101301233110121000220031120031 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_637_F3 +T22113312122202103031023120301031110 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_641_F3 +T13031301101121223221212020032131113 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_692_F3 +T01122320200330103121202301211100220 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff -r 19d8ba4269ba -r 8bd2ace6c92d test-data/fastq_combiner_no_qual_ascii_out_1.fastqsolid --- a/test-data/fastq_combiner_no_qual_ascii_out_1.fastqsolid Tue Mar 02 09:51:05 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,576 +0,0 @@ -@1831_573_1004_F3 -T00030133312212111300011021310132222 -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@1831_573_1050_F3 -T03330322230322112131010221102122113 -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@1831_573_1067_F3 -T00023032023103330112220321200200002 -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@1831_573_1219_F3 -T11211130300300301021212330201121310 -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@1831_573_1242_F3 -T02132003121011302100130302112221121 -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@1831_573_1333_F3 -T00200312330110101013212313222303112 -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@1831_573_1362_F3 -T21203131001102231121211101111321131 -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@1831_573_1448_F3 -T23101211223113320132212331313312022 -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@1831_573_1490_F3