| Next changeset 1:e711d52c7509 (2015-11-11) |
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Commit message:
Imported from capsule None |
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added:
fastq_combiner.py fastq_combiner.xml test-data/combine_phiX_out_1.fastqcssanger test-data/combine_phiX_out_2.fastqcssanger test-data/fastq_combiner_in_1.fasta test-data/fastq_combiner_in_1.qual454 test-data/fastq_combiner_no_qual_ascii_out_1.fastqcssanger test-data/fastq_combiner_no_qual_decimal_out_1.fastqsanger test-data/s2fq_phiX.csfasta test-data/s2fq_phiX.qualsolid test-data/wrapping_as_sanger.fastqsanger test-data/wrapping_as_sanger_decimal.fastqsanger tool_dependencies.xml |
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| diff -r 000000000000 -r 94306bdd58f7 fastq_combiner.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq_combiner.py Mon Jan 27 09:28:39 2014 -0500 |
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| @@ -0,0 +1,49 @@ +#Dan Blankenberg +import sys, os, shutil +from galaxy_utils.sequence.fastq import fastqWriter, fastqSequencingRead, fastqCombiner, fastqFakeFastaScoreReader +from galaxy_utils.sequence.fasta import fastaReader, fastaNamedReader + +def main(): + #Read command line arguments + fasta_filename = sys.argv[1] + fasta_type = sys.argv[2] or 'fasta' #should always be fasta or csfasta? what if txt? + qual_filename = sys.argv[3] + qual_type = sys.argv[4] or 'qualsanger' #qual454 qualsolid + output_filename = sys.argv[5] + force_quality_encoding = sys.argv[6] + if force_quality_encoding == 'None': + force_quality_encoding = None + + format = 'sanger' + if fasta_type == 'csfasta' or qual_type == 'qualsolid': + format = 'cssanger' + elif qual_type == 'qualsolexa': + format = 'solexa' + elif qual_type == 'qualillumina': + format = 'illumina' + + out = fastqWriter( open( output_filename, 'wb' ), format = format, force_quality_encoding = force_quality_encoding ) + if qual_filename == 'None': + qual_input = fastqFakeFastaScoreReader( format, quality_encoding = force_quality_encoding ) + else: + qual_input = fastaNamedReader( open( qual_filename, 'rb' ) ) + + fastq_combiner = fastqCombiner( format ) + i = None + skip_count = 0 + for i, sequence in enumerate( fastaReader( open( fasta_filename, 'rb' ) ) ): + quality = qual_input.get( sequence ) + if quality: + fastq_read = fastq_combiner.combine( sequence, quality ) + out.write( fastq_read ) + else: + skip_count += 1 + out.close() + if i is None: + print "Your file contains no valid FASTA sequences." + else: + print qual_input.has_data() + print 'Combined %s of %s sequences with quality scores (%.2f%%).' % ( i - skip_count + 1, i + 1, float( i - skip_count + 1 ) / float( i + 1 ) * 100.0 ) + +if __name__ == "__main__": + main() |
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| diff -r 000000000000 -r 94306bdd58f7 fastq_combiner.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq_combiner.xml Mon Jan 27 09:28:39 2014 -0500 |
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| @@ -0,0 +1,80 @@ +<tool id="fastq_combiner" name="Combine FASTA and QUAL" version="1.0.1"> + <description>into FASTQ</description> + <requirements> + <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> + </requirements> + <command interpreter="python">fastq_combiner.py '$fasta_file' '${fasta_file.extension}' '$qual_file' '${qual_file.extension}' '$output_file' '$force_quality_encoding'</command> + <inputs> + <param name="fasta_file" type="data" format="fasta,csfasta" label="FASTA File" /> + <param name="qual_file" type="data" format="qual" label="Quality Score File" optional="True" /> + <param name="force_quality_encoding" type="select" label="Force Quality Score encoding"> + <option value="None">Use Source Encoding</option> + <option value="ascii" selected="True">ASCII</option> + <option value="decimal">Decimal</option> + </param> + </inputs> + <outputs> + <data name="output_file" format="fastqsanger"> + <change_format> + <when input_dataset="fasta_file" attribute="extension" value="csfasta" format="fastqcssanger" /> + <when input_dataset="qual_file" attribute="extension" value="qualsolid" format="fastqcssanger" /> + <when input_dataset="qual_file" attribute="extension" value="qualsolexa" format="fastqsolexa" /> + <when input_dataset="qual_file" attribute="extension" value="qualillumina" format="fastqillumina" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" /> + <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" /> + <param name="force_quality_encoding" value="None" /> + <output name="output_file" file="combine_phiX_out_1.fastqcssanger" /> + </test> + <test> + <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" /> + <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" /> + <param name="force_quality_encoding" value="ascii" /> + <output name="output_file" file="combine_phiX_out_2.fastqcssanger" /> + </test> + <test> + <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" /> + <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" /> + <param name="force_quality_encoding" value="None" /> + <output name="output_file" file="wrapping_as_sanger.fastqsanger" /> + </test> + <test> + <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" /> + <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" /> + <param name="force_quality_encoding" value="decimal" /> + <output name="output_file" file="wrapping_as_sanger_decimal.fastqsanger" /> + </test> + <test> + <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" /> + <param name="qual_file" /> + <param name="force_quality_encoding" value="decimal" /> + <output name="output_file" file="fastq_combiner_no_qual_decimal_out_1.fastqsanger" /> + </test> + <test> + <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" /> + <param name="qual_file" /> + <param name="force_quality_encoding" value="ascii" /> + <output name="output_file" file="fastq_combiner_no_qual_ascii_out_1.fastqcssanger" /> + </test> + </tests> + <help> +**What it does** + +This tool joins a FASTA file to a Quality Score file, creating a single FASTQ block for each read. + +Specifying a set of quality scores is optional; when not provided, the output will be fastqsanger or fastqcssanger (when a csfasta is provided) with each quality score being the maximal allowed value (93). + +Use this tool, for example, to convert 454-type output to FASTQ. + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help> +</tool> |
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| diff -r 000000000000 -r 94306bdd58f7 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 Mon Jan 27 09:28:39 2014 -0500 |
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| diff -r 000000000000 -r 94306bdd58f7 test-data/combine_phiX_out_2.fastqcssanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combine_phiX_out_2.fastqcssanger Mon Jan 27 09:28:39 2014 -0500 |
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| b"@@ -0,0 +1,576 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|
| b |
| diff -r 000000000000 -r 94306bdd58f7 test-data/fastq_combiner_in_1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_combiner_in_1.fasta Mon Jan 27 09:28:39 2014 -0500 |
| b |
| @@ -0,0 +1,14 @@ +>SRR014849.50939 EIXKN4201BA2EC length=135 +GAAATTTCAGGGCCACCTTTTTTTT +GATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGA +GAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG +>SRR014849.110027 EIXKN4201APUB0 length=131 +CTTCAAATGATTC +CGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCC +TTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGAC +CAGAACGATCCG +>SRR014849.203935 EIXKN4201B4HU6 length=144 +AACCCGTCCCA +TCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACC +CCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTT +TAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT |
| b |
| diff -r 000000000000 -r 94306bdd58f7 test-data/fastq_combiner_in_1.qual454 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_combiner_in_1.qual454 Mon Jan 27 09:28:39 2014 -0500 |
| b |
| @@ -0,0 +1,22 @@ +>SRR014849.110027 EIXKN4201APUB0 length=131 +=B::@<':=5A9?7EA0:=<<?6@7<3?5< +@;%D?-B=)::0=4<D? +-EA/D@2";B;B: +B:A9;;=<B;;<B;<B;<B;:A;<A;8FB7 ++=<B;B:A9<1:=FB6(<=<<EA0956;<2 +==A8===:@8= +>SRR014849.203935 EIXKN4201B4HU6 length=144 +A;@;%75?:#<<9EA1;=EA3%B;B;A;B; +@;%9EA1EA1EA3%<B;A;8EA0D@ +3$EA1 +=B;A;B;B;:=:B;:B:A9:EA0A9<FA81 ++&"D?-B;4<::/<;=:A98-5?6=C>+8< +<3;=4:DA3%<;=8-9.A=):B=* +>SRR014849.50939 EIXKN4201BA2EC length=135 +;C?-EA/=<EA/B;<B;D>60,)%"<=:5< +@8<B;=B;<;E +A4'@8FB6*<:=<<===<= +;=B:A9<<B;=B;=EA0:<B:<<=<<FA81 ++$?6;<A9=<3>5@7@8<A<(B=*A=)<<2 +?57B=*B=*D?-:=4 + |
| b |
| diff -r 000000000000 -r 94306bdd58f7 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 Mon Jan 27 09:28:39 2014 -0500 |
| b |
| b'@@ -0,0 +1,576 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|
| b |
| diff -r 000000000000 -r 94306bdd58f7 test-data/fastq_combiner_no_qual_decimal_out_1.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_combiner_no_qual_decimal_out_1.fastqsanger Mon Jan 27 09:28:39 2014 -0500 |
| b |
| @@ -0,0 +1,12 @@ +@SRR014849.50939 EIXKN4201BA2EC length=135 +GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG ++ +93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 +@SRR014849.110027 EIXKN4201APUB0 length=131 +CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG ++ +93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 +@SRR014849.203935 EIXKN4201B4HU6 length=144 +AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT ++ +93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 |
| b |
| diff -r 000000000000 -r 94306bdd58f7 test-data/s2fq_phiX.csfasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_phiX.csfasta Mon Jan 27 09:28:39 2014 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r 94306bdd58f7 test-data/s2fq_phiX.qualsolid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_phiX.qualsolid Mon Jan 27 09:28:39 2014 -0500 |
| b |
| b'@@ -0,0 +1,288 @@\n+>1831_573_1004_F3\n+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 \n+>1831_573_1050_F3\n+8 26 31 31 16 22 30 31 28 29 22 30 30 31 32 23 30 28 28 31 19 32 30 32 19 8 5 10 13 6 5 10 6 16 11 \n+>1831_573_1067_F3\n+13 10 10 2 4 7 6 11 4 14 3 11 10 5 16 2 5 8 11 8 5 10 6 9 6 9 4 2 3 5 2 4 7 6 3 \n+>1831_573_1219_F3\n+31 31 31 28 19 14 10 8 20 8 19 15 23 30 6 21 21 20 29 9 14 20 30 27 21 16 6 26 27 18 11 25 11 20 12 \n+>1831_573_1242_F3\n+29 29 29 25 25 29 16 22 28 32 20 30 31 31 28 26 22 32 28 26 17 13 21 15 29 23 17 27 23 28 22 19 10 26 26 \n+>1831_573_1333_F3\n+8 28 6 31 2 4 18 28 13 29 8 14 18 19 9 16 16 22 11 11 14 21 12 19 10 13 24 22 19 17 19 20 21 27 8 \n+>1831_573_1362_F3\n+34 33 31 31 30 31 31 30 31 34 31 33 32 30 31 29 31 27 31 23 32 31 30 31 6 13 23 6 30 16 22 25 11 10 30 \n+>1831_573_1448_F3\n+22 22 28 32 8 30 11 13 31 32 31 31 25 31 31 27 28 14 22 8 31 27 12 2 23 21 21 17 4 24 21 16 18 5 10 \n+>1831_573_1490_F3\n+31 31 31 31 30 11 31 30 30 31 3 29 27 28 29 10 4 14 9 29 9 16 11 8 30 17 21 5 16 17 6 24 4 22 13 \n+>1831_573_1523_F3\n+7 11 14 14 9 11 2 23 6 6 13 21 6 6 21 6 17 5 17 22 14 23 15 8 4 5 2 15 6 4 2 9 11 17 6 \n+>1831_573_1578_F3\n+31 30 28 31 27 31 34 31 30 31 31 30 30 28 29 31 26 22 27 27 23 27 21 24 19 8 18 20 16 16 7 10 16 27 13 \n+>1831_573_1647_F3\n+28 30 31 31 27 31 31 30 30 30 26 32 28 28 31 31 26 24 30 31 30 18 28 26 21 13 19 14 26 21 25 28 14 26 19 \n+>1831_573_1684_F3\n+22 29 16 25 23 27 31 18 24 31 31 30 30 24 28 26 31 31 27 29 30 31 31 27 26 27 30 22 29 22 21 30 24 29 30 \n+>1831_573_1769_F3\n+22 20 19 22 19 24 5 5 22 21 22 4 14 22 26 18 3 12 22 26 18 2 11 18 14 14 2 11 19 20 14 2 5 15 21 \n+>1831_573_1853_F3\n+21 19 13 14 33 31 31 22 17 33 10 14 19 30 31 30 22 30 10 31 24 14 10 24 24 13 6 8 17 27 17 5 8 17 5 \n+>1831_573_1943_F3\n+7 29 14 9 16 11 8 11 31 12 8 6 15 9 29 20 6 3 14 30 21 31 14 13 5 30 23 14 7 6 8 32 19 18 11 \n+>1831_573_1977_F3\n+31 31 30 21 31 23 31 31 24 32 31 28 19 21 18 18 32 22 30 24 30 27 18 25 10 22 29 6 31 4 31 30 4 18 17 \n+>1831_574_109_F3\n+15 22 21 20 16 2 19 23 16 22 29 31 21 20 27 17 25 23 19 22 16 21 28 22 23 23 27 16 24 24 20 13 22 30 21 \n+>1831_574_148_F3\n+27 26 12 29 18 26 26 18 29 14 14 29 15 26 26 22 28 11 28 19 12 19 14 10 29 15 17 24 27 24 27 21 17 19 26 \n+>1831_574_185_F3\n+31 27 19 26 4 4 31 22 29 2 9 29 24 22 4 21 26 10 23 3 2 27 15 22 4 16 18 22 17 3 4 27 20 19 2 \n+>1831_574_243_F3\n+2 31 31 31 24 20 31 28 24 30 9 29 27 19 20 3 27 31 27 19 4 31 24 30 22 2 28 30 29 22 5 29 30 24 22 \n+>1831_574_257_F3\n+4 29 29 33 29 8 31 30 29 33 31 33 30 31 16 4 9 4 11 2 10 15 15 13 6 7 10 5 20 5 4 2 3 18 5 \n+>1831_574_293_F3\n+5 6 8 22 6 13 9 4 2 5 3 6 14 13 3 2 2 3 13 3 5 9 8 10 9 3 2 23 4 5 4 2 5 5 4 \n+>1831_574_389_F3\n+8 8 3 29 14 29 23 8 25 17 31 25 17 16 18 26 26 13 16 8 31 18 4 21 19 4 10 8 27 22 8 10 3 24 17 \n+>1831_574_575_F3\n+22 30 31 29 28 30 31 29 23 31 31 31 28 31 21 9 4 5 27 28 6 20 31 27 27 6 11 15 27 28 19 9 20 14 27 \n+>1831_574_592_F3\n+22 18 12 20 8 16 24 11 11 27 31 29 19 15 21 22 27 17 13 12 23 21 19 18 19 21 26 24 27 16 14 26 17 16 17 \n+>1831_574_617_F3\n+31 29 31 30 26 29 30 28 31 28 28 31 29 31 28 20 30 31 10 31 25 31 19 15 31 29 27 25 15 8 6 8 21 19 12 \n+>1831_574_725_F3\n+24 6 29 30 20 17 10 20 28 26 19 3 21 26 27 23 13 16 27 19 22 9 24 10 30 22 7 10 20 26 12 8 13 8 19 \n+>1831_574_734_F3\n+13 12 5 13 3 17 5 27 9 7 12 4 8 25 14 8 4 20 25 8 14 4 22 10 11 24 15 18 19 9 32 13 30 22 15 \n+>1831_574_824_F3\n+26 31 31 31 26 26 8 11 10 31 27 12 27 22 26 27 5 23 24 30 30 5 17 24 30 27 3 17 25 32 27 8 26 23 30 \n+>1831_574_959_F3\n+22 32 28 26 10 30 31 24 26 14 27 31 26 27 23 2 5 5 14 9 4 7 4 13 15 3 15 3 17 8 10 16 3 12 16 \n+>1831_574_1062_F3\n+19 31 23 17 16 27 14 14 25 16 18 21 14 23 27 16 14 20 13 19 17 22 13 26 29 17 23 23 14 15 27 16 3 8 14 \n+>1831_574_1092_F3\n+27 23 30 13 11 24 23 8 15 18 4 2 11 11 11 7 11 10 10 3 6 21 24 6 2 24 6 22 2 6 26 21 13 4 17 \n+>1831_574_1103_F3\n+31 30 30 29 30 31 28 29 31 31 32 27 29 30 28 31 28 28 2'..b' 17 27 \n+>1831_576_1168_F3\n+29 31 34 34 21 31 31 17 30 24 28 29 22 30 26 22 21 27 26 19 21 22 31 26 24 11 15 4 17 21 6 6 11 19 3 \n+>1831_576_1207_F3\n+4 3 29 17 11 7 5 30 19 30 7 11 31 25 27 5 11 31 29 30 3 5 25 23 32 4 4 28 15 13 4 11 20 24 22 \n+>1831_576_1289_F3\n+31 24 27 29 16 33 31 31 26 22 31 31 21 21 18 28 28 17 23 11 20 6 25 23 27 27 11 13 28 17 29 29 13 20 15 \n+>1831_576_1329_F3\n+27 29 5 15 11 23 22 15 14 32 31 31 14 20 13 26 28 26 25 6 5 31 18 6 5 3 3 4 11 10 2 7 3 5 17 \n+>1831_576_1367_F3\n+30 30 31 31 27 29 31 31 28 31 27 31 27 28 31 29 31 30 30 24 25 30 27 28 29 28 27 23 26 20 24 31 22 23 22 \n+>1831_576_1416_F3\n+10 6 26 30 13 13 16 13 27 31 6 13 28 10 21 13 20 30 22 27 15 12 30 22 26 7 4 28 29 20 21 13 24 23 31 \n+>1831_576_1461_F3\n+2 16 5 22 19 2 7 2 7 5 2 2 3 2 11 6 2 2 2 4 2 4 4 2 9 2 5 4 4 2 2 4 4 4 6 \n+>1831_576_1605_F3\n+21 27 31 34 31 31 29 16 26 31 25 26 27 27 31 31 24 31 30 30 30 24 27 18 30 20 12 17 16 28 19 23 22 22 11 \n+>1831_576_1664_F3\n+31 31 30 29 30 31 28 32 25 31 31 29 31 28 6 28 27 29 28 8 13 29 28 24 9 23 8 7 22 2 14 10 10 26 8 \n+>1831_576_1671_F3\n+31 31 30 31 20 29 31 31 23 5 23 30 17 20 2 5 8 5 20 5 5 8 16 20 5 5 11 5 19 4 5 11 5 21 4 \n+>1831_576_1729_F3\n+31 30 31 30 27 30 27 31 29 32 30 14 28 28 30 29 30 22 29 30 31 23 27 30 31 29 24 24 26 29 27 10 15 28 29 \n+>1831_576_1880_F3\n+15 20 16 20 14 22 24 17 11 25 11 22 14 4 14 15 20 11 4 3 8 25 10 2 23 4 17 7 16 22 20 19 8 8 18 \n+>1831_576_1982_F3\n+11 31 31 30 31 11 32 29 27 31 24 31 28 30 31 24 33 28 23 27 21 31 31 21 31 17 27 32 30 29 13 22 27 10 31 \n+>1831_576_1987_F3\n+8 2 2 7 8 7 2 5 2 2 8 4 8 14 12 2 4 3 16 16 2 4 18 29 6 2 2 5 3 11 2 3 3 6 10 \n+>1831_576_2014_F3\n+31 31 31 24 11 33 17 24 12 20 29 6 30 11 10 30 22 24 10 14 32 6 26 6 17 31 6 20 5 14 24 11 21 5 16 \n+>1831_576_2028_F3\n+20 27 29 24 29 20 6 17 7 5 22 15 22 13 23 2 5 5 18 24 11 15 4 22 14 2 7 2 11 9 4 5 20 9 10 \n+>1831_577_40_F3\n+24 17 14 19 7 6 13 6 8 7 27 9 30 2 3 8 4 5 27 11 14 18 24 27 7 13 17 11 10 27 28 31 21 16 16 \n+>1831_577_119_F3\n+24 29 30 34 16 16 8 12 16 14 8 2 26 2 14 11 23 20 15 9 10 13 10 3 3 20 20 20 15 10 4 12 13 19 15 \n+>1831_577_133_F3\n+14 19 31 29 29 30 28 16 30 25 10 29 31 15 22 31 31 29 27 29 31 9 27 10 16 31 16 20 8 24 21 6 17 3 8 \n+>1831_577_255_F3\n+22 27 28 23 22 31 29 21 24 4 9 9 2 5 2 12 10 3 13 2 5 5 2 10 3 12 10 4 5 4 13 11 4 20 2 \n+>1831_577_281_F3\n+22 12 25 33 26 23 31 28 26 29 22 31 29 19 30 28 30 10 21 20 24 30 26 20 27 22 30 26 24 31 23 7 29 25 30 \n+>1831_577_288_F3\n+20 26 14 22 24 30 30 5 28 33 25 25 17 24 23 9 21 13 22 14 10 19 5 17 16 11 22 11 21 30 13 22 2 6 21 \n+>1831_577_322_F3\n+24 28 26 29 19 20 15 21 26 17 20 20 19 21 19 12 27 2 22 10 16 24 19 5 17 27 30 21 20 24 21 23 8 22 14 \n+>1831_577_362_F3\n+21 17 33 30 25 31 30 31 27 30 24 20 23 28 11 18 25 11 24 15 25 5 6 12 24 24 11 21 27 20 13 7 3 10 21 \n+>1831_577_382_F3\n+16 17 24 20 22 14 25 16 8 8 28 22 21 7 9 17 19 26 11 18 10 25 27 13 5 13 5 12 28 16 28 17 14 20 9 \n+>1831_577_464_F3\n+18 28 27 22 14 27 23 17 21 8 29 2 13 6 5 19 17 15 19 10 20 2 14 15 19 16 13 22 9 24 16 5 22 20 21 \n+>1831_577_488_F3\n+25 19 23 13 11 9 29 21 20 21 21 27 30 23 28 27 28 27 17 29 21 26 24 19 29 26 28 24 29 31 23 24 17 19 31 \n+>1831_577_511_F3\n+2 22 14 10 5 3 25 27 22 4 21 11 3 3 4 6 4 14 10 8 2 3 22 7 7 5 9 18 29 16 21 6 15 14 10 \n+>1831_577_545_F3\n+29 29 27 27 24 30 27 29 30 32 27 19 23 16 31 27 31 23 28 28 31 22 21 14 21 16 27 24 20 13 20 24 23 23 12 \n+>1831_577_559_F3\n+13 27 31 26 30 30 31 29 31 30 14 17 27 13 31 16 28 29 16 17 28 21 16 14 26 28 30 13 5 17 10 24 17 8 6 \n+>1831_577_562_F3\n+2 7 7 5 9 5 15 4 8 16 4 8 2 7 3 17 12 11 9 9 9 4 14 12 11 11 8 8 5 11 12 13 16 6 9 \n+>1831_577_637_F3\n+23 12 11 19 2 29 25 12 21 10 25 23 11 5 7 20 26 18 28 15 29 22 28 21 23 5 16 14 24 5 6 30 26 19 11 \n+>1831_577_641_F3\n+5 19 22 26 14 6 25 32 26 26 20 30 25 22 17 11 7 28 8 11 2 9 30 10 13 2 5 22 3 23 2 4 22 14 6 \n+>1831_577_692_F3\n+31 33 11 31 30 31 33 7 31 32 30 31 10 31 31 29 31 10 30 28 29 31 6 28 27 31 27 28 27 24 28 30 22 20 27\n' |
| b |
| diff -r 000000000000 -r 94306bdd58f7 test-data/wrapping_as_sanger.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/wrapping_as_sanger.fastqsanger Mon Jan 27 09:28:39 2014 -0500 |
| b |
| @@ -0,0 +1,12 @@ +@SRR014849.50939 EIXKN4201BA2EC length=135 +GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG ++ +;C?-EA/=<EA/B;<B;D>60,)%"<=:5<@8<B;=B;<;EA4'@8FB6*<:=<<===<=;=B:A9<<B;=B;=EA0:<B:<<=<<FA81+$?6;<A9=<3>5@7@8<A<(B=*A=)<<2?57B=*B=*D?-:=4 +@SRR014849.110027 EIXKN4201APUB0 length=131 +CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG ++ +=B::@<':=5A9?7EA0:=<<?6@7<3?5<@;%D?-B=)::0=4<D?-EA/D@2";B;B:B:A9;;=<B;;<B;<B;<B;:A;<A;8FB7+=<B;B:A9<1:=FB6(<=<<EA0956;<2==A8===:@8= +@SRR014849.203935 EIXKN4201B4HU6 length=144 +AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT ++ +A;@;%75?:#<<9EA1;=EA3%B;B;A;B;@;%9EA1EA1EA3%<B;A;8EA0D@3$EA1=B;A;B;B;:=:B;:B:A9:EA0A9<FA81+&"D?-B;4<::/<;=:A98-5?6=C>+8<<3;=4:DA3%<;=8-9.A=):B=* |
| b |
| diff -r 000000000000 -r 94306bdd58f7 test-data/wrapping_as_sanger_decimal.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/wrapping_as_sanger_decimal.fastqsanger Mon Jan 27 09:28:39 2014 -0500 |
| b |
| @@ -0,0 +1,12 @@ +@SRR014849.50939 EIXKN4201BA2EC length=135 +GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG ++ +26 34 30 12 36 32 14 28 27 36 32 14 33 26 27 33 26 35 29 21 15 11 8 4 1 27 28 25 20 27 31 23 27 33 26 28 33 26 27 26 36 32 19 6 31 23 37 33 21 9 27 25 28 27 27 28 28 28 27 28 26 28 33 25 32 24 27 27 33 26 28 33 26 28 36 32 15 25 27 33 25 27 27 28 27 27 37 32 23 16 10 3 30 21 26 27 32 24 28 27 18 29 20 31 22 31 23 27 32 27 7 33 28 9 32 28 8 27 27 17 30 20 22 33 28 9 33 28 9 35 30 12 25 28 19 +@SRR014849.110027 EIXKN4201APUB0 length=131 +CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG ++ +28 33 25 25 31 27 6 25 28 20 32 24 30 22 36 32 15 25 28 27 27 30 21 31 22 27 18 30 20 27 31 26 4 35 30 12 33 28 8 25 25 15 28 19 27 35 30 12 36 32 14 35 31 17 1 26 33 26 33 25 33 25 32 24 26 26 28 27 33 26 26 27 33 26 27 33 26 27 33 26 25 32 26 27 32 26 23 37 33 22 10 28 27 33 26 33 25 32 24 27 16 25 28 37 33 21 7 27 28 27 27 36 32 15 24 20 21 26 27 17 28 28 32 23 28 28 28 25 31 23 28 +@SRR014849.203935 EIXKN4201B4HU6 length=144 +AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT ++ +32 26 31 26 4 22 20 30 25 2 27 27 24 36 32 16 26 28 36 32 18 4 33 26 33 26 32 26 33 26 31 26 4 24 36 32 16 36 32 16 36 32 18 4 27 33 26 32 26 23 36 32 15 35 31 18 3 36 32 16 28 33 26 32 26 33 26 33 26 25 28 25 33 26 25 33 25 32 24 25 36 32 15 32 24 27 37 32 23 16 10 5 1 35 30 12 33 26 19 27 25 25 14 27 26 28 25 32 24 23 12 20 30 21 28 34 29 10 23 27 27 18 26 28 19 25 35 32 18 4 27 26 28 23 12 24 13 32 28 8 25 33 28 9 |
| b |
| diff -r 000000000000 -r 94306bdd58f7 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jan 27 09:28:39 2014 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="galaxy_sequence_utils" version="1.0.0"> + <repository changeset_revision="0643676ad5f7" name="package_galaxy_utils_1_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |