# HG changeset patch # User devteam # Date 1390832919 18000 # Node ID 94306bdd58f7eb43dddb3ed9f1e9a2be9ffb3a2c Imported from capsule None 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 @@ -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() 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 @@ -0,0 +1,80 @@ + + into FASTQ + + galaxy_sequence_utils + + fastq_combiner.py '$fasta_file' '${fasta_file.extension}' '$qual_file' '${qual_file.extension}' '$output_file' '$force_quality_encoding' + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**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>`_ + + + 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 @@ -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 32 30 32 19 8 5 10 13 6 5 10 6 16 11 +@1831_573_1067_F3 +T00023032023103330112220321200200002 ++ +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 +@1831_573_1219_F3 +T11211130300300301021212330201121310 ++ +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 +@1831_573_1242_F3 +T02132003121011302100130302112221121 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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 @@ -0,0 +1,12 @@ +@SRR014849.50939 EIXKN4201BA2EC length=135 +GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG ++ +;C?-EA/=60,)%"<=:5<@85@7@8+8<<3;=4:DA3%<;=8-9.A=):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 @@ -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 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 @@ -0,0 +1,6 @@ + + + + + +