| Next changeset 1:462abc5618ba (2017-09-30) |
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Commit message:
Imported from capsule None |
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added:
fastq_paired_end_deinterlacer.py fastq_paired_end_deinterlacer.xml test-data/paired_end_1.fastqsanger test-data/paired_end_1_cleaned.fastqsanger test-data/paired_end_1_cleaned_singles.fastqsanger test-data/paired_end_1_singles.fastqsanger test-data/paired_end_2.fastqsanger test-data/paired_end_2_cleaned.fastqsanger test-data/paired_end_2_cleaned_singles.fastqsanger test-data/paired_end_2_singles.fastqsanger test-data/paired_end_merged.fastqsanger test-data/paired_end_merged_errors.fastqsanger tool_dependencies.xml |
| b |
| diff -r 000000000000 -r f0949bc49926 fastq_paired_end_deinterlacer.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq_paired_end_deinterlacer.py Mon Jan 27 09:27:16 2014 -0500 |
| [ |
| @@ -0,0 +1,66 @@ +#Florent Angly +import sys +from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqNamedReader, fastqJoiner + +def main(): + input_filename = sys.argv[1] + input_type = sys.argv[2] or 'sanger' + mate1_filename = sys.argv[3] + mate2_filename = sys.argv[4] + single1_filename = sys.argv[5] + single2_filename = sys.argv[6] + + type = input_type + input = fastqNamedReader( open( input_filename, 'rb' ), format = type ) + mate1_out = fastqWriter( open( mate1_filename, 'wb' ), format = type ) + mate2_out = fastqWriter( open( mate2_filename, 'wb' ), format = type ) + single1_out = fastqWriter( open( single1_filename, 'wb' ), format = type ) + single2_out = fastqWriter( open( single2_filename, 'wb' ), format = type ) + joiner = fastqJoiner( type ) + + i = None + skip_count = 0 + found = {} + for i, read in enumerate( fastqReader( open( input_filename, 'rb' ), format = type ) ): + + if read.identifier in found: + del found[read.identifier] + continue + + mate1 = input.get( read.identifier ) + + mate2 = input.get( joiner.get_paired_identifier( mate1 ) ) + + if mate2: + # This is a mate pair + found[mate2.identifier] = None + if joiner.is_first_mate( mate1 ): + mate1_out.write( mate1 ) + mate2_out.write( mate2 ) + else: + mate1_out.write( mate2 ) + mate2_out.write( mate1 ) + else: + # This is a single + skip_count += 1 + if joiner.is_first_mate( mate1 ): + single1_out.write( mate1 ) + else: + single2_out.write( mate1 ) + + if i is None: + print "Your input file contained no valid FASTQ sequences." + else: + if skip_count: + print 'There were %i reads with no mate.' % skip_count + print 'De-interlaced %s pairs of sequences.' % ( (i - skip_count + 1)/2 ) + + input.close() + mate1_out.close() + mate2_out.close() + single1_out.close() + single2_out.close() + + +if __name__ == "__main__": + main() |
| b |
| diff -r 000000000000 -r f0949bc49926 fastq_paired_end_deinterlacer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq_paired_end_deinterlacer.xml Mon Jan 27 09:27:16 2014 -0500 |
| [ |
| @@ -0,0 +1,73 @@ +<tool id="fastq_paired_end_deinterlacer" name="FASTQ de-interlacer" version="1.1"> + <description>on paired end reads</description> + <requirements> + <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> + </requirements> + <command interpreter="python">fastq_paired_end_deinterlacer.py '$input_file' '${input_file.extension[len( 'fastq' ):]}' '$output1_pairs_file' '$output2_pairs_file' '$output1_singles_file' '$output2_singles_file'</command> + <inputs> + <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ reads" /> + </inputs> + <outputs> + <data name="output1_pairs_file" format="input" label="FASTQ de-interlacer left mates from data ${input_file.hid}" /> + <data name="output2_pairs_file" format="input" label="FASTQ de-interlacer right mates from data ${input_file.hid}"/> + <data name="output1_singles_file" format="input" label="FASTQ de-interlacer left singles from data ${input_file.hid}"/> + <data name="output2_singles_file" format="input" label="FASTQ de-interlacer right singles from data ${input_file.hid}"/> + </outputs> + <tests> + <test> + <param name="input_file" value="paired_end_merged.fastqsanger" ftype="fastqsanger" /> + <output name="output1_pairs_file" file="paired_end_1.fastqsanger" /> + <output name="output2_pairs_file" file="paired_end_2.fastqsanger" /> + <output name="output1_singles_file" file="paired_end_1_singles.fastqsanger" /> + <output name="output2_singles_file" file="paired_end_2_singles.fastqsanger" /> + </test> + <test> + <param name="input_file" value="paired_end_merged_errors.fastqsanger" ftype="fastqsanger" /> + <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" /> + <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" /> + <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" /> + <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" /> + </test> + </tests> + <help> +**What it does** + +De-interlaces a single fastq dataset representing paired-end run into two fastq datasets containing only the first or second mate read. Reads without mate are saved in separate output files. + +Sequence identifiers for paired-end reads must follow the /1 and /2 convention. + +----- + +**Input** + +A multiple-fastq file containing paired-end reads, for example:: + + @1539:931/1 + ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG + +1539:931/1 + BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB + @1539:931/2 + CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT + +1539:931/2 + WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB + +----- + +**Output** + +Multi-fastq file with left-hand mate only:: + + @1539:931/1 + ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG + +1539:931/1 + BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB + +Multi-fastq file with right-hand mate only:: + + @1539:931/2 + CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT + +1539:931/2 + WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB + + </help> +</tool> |
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| diff -r 000000000000 -r f0949bc49926 test-data/paired_end_1.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_end_1.fastqsanger Mon Jan 27 09:27:16 2014 -0500 |
| [ |
| @@ -0,0 +1,20 @@ +@1539:931/1 +NACATCAACACTCAGTAACGGCTGGCGCAAAATGGCATTGATTAACGAAGACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG ++1539:931/1 +BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@2971:937/1 +NCGGAGACTTCGAGGCCATCCAGTCGATTGCCAAAGTCATCAAGGGGTCGACGATCTGCTCCCTTGCCCGTTCCAACGAGAATGAAATCCGCCGCGCGTGG ++2971:937/1 +BMQMMRRRSS__________XXXXXVVVVV_b___Y[Y[YXVRVWWPWVX_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@3786:949/1 +NTACCGCGCAACGGCATGATGGCTTGGAACTCACGGTCACGCGCCTGTTTGGCAGAGCCGCCCGCCGAGTCACCTTCCACTAGGAACAGTTCGGAGCGGTT ++3786:949/1 +BKGGKKJNJJ_______W__Y__W_TVPVP[YY[[_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@4205:944/1 +NGATCTGGGCTTCAGCAAGACCGATGTCGGCGTGATTGCCAAGCATGCCGGACTCTGGCCGGCGGGGTTCGGCGGTGTGCTGGGTGGCTTGGGGGTGGGGG ++4205:944/1 +BLLLLTWTTR_V_______TYYYRYYYYYY____VWRWWW___BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@4534:934/1 +NAATGCCGGTATTTGGCACGATGGCGGCACGCTTCCACGACGACGGGGTGACCTCTCTCTATCAGGCGATGGCATCCAAATTGCACGCGCGGGGTTTGAGG ++4534:934/1 +BGGFGLJLJL______________V____________________YYYPQOTWVT__________BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB |
| b |
| diff -r 000000000000 -r f0949bc49926 test-data/paired_end_1_cleaned.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_end_1_cleaned.fastqsanger Mon Jan 27 09:27:16 2014 -0500 |
| [ |
| @@ -0,0 +1,16 @@ +@2971:937/1 +NCGGAGACTTCGAGGCCATCCAGTCGATTGCCAAAGTCATCAAGGGGTCGACGATCTGCTCCCTTGCCCGTTCCAACGAGAATGAAATCCGCCGCGCGTGG ++2971:937/1 +BMQMMRRRSS__________XXXXXVVVVV_b___Y[Y[YXVRVWWPWVX_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@3786:949/1 +NTACCGCGCAACGGCATGATGGCTTGGAACTCACGGTCACGCGCCTGTTTGGCAGAGCCGCCCGCCGAGTCACCTTCCACTAGGAACAGTTCGGAGCGGTT ++3786:949/1 +BKGGKKJNJJ_______W__Y__W_TVPVP[YY[[_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@4205:944/1 +NGATCTGGGCTTCAGCAAGACCGATGTCGGCGTGATTGCCAAGCATGCCGGACTCTGGCCGGCGGGGTTCGGCGGTGTGCTGGGTGGCTTGGGGGTGGGGG ++4205:944/1 +BLLLLTWTTR_V_______TYYYRYYYYYY____VWRWWW___BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@4534:934/1 +NAATGCCGGTATTTGGCACGATGGCGGCACGCTTCCACGACGACGGGGTGACCTCTCTCTATCAGGCGATGGCATCCAAATTGCACGCGCGGGGTTTGAGG ++4534:934/1 +BGGFGLJLJL______________V____________________YYYPQOTWVT__________BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB |
| b |
| diff -r 000000000000 -r f0949bc49926 test-data/paired_end_1_cleaned_singles.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_end_1_cleaned_singles.fastqsanger Mon Jan 27 09:27:16 2014 -0500 |
| b |
| @@ -0,0 +1,4 @@ +@1539:931/1 +NACATCAACACTCAGTAACGGCTGGCGCAAAATGGCATTGATTAACGAAGACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG ++1539:931/1 +BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB |
| b |
| diff -r 000000000000 -r f0949bc49926 test-data/paired_end_2.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_end_2.fastqsanger Mon Jan 27 09:27:16 2014 -0500 |
| [ |
| @@ -0,0 +1,20 @@ +@1539:931/2 this read has a description +GCGCGTAACGTTTCACCTCGAGATCGTTGTCGGCCGCAATCTCCTGGGGGCGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT ++1539:931/2 this read has a description +aee_dcadeeWcaaadJbdaff[fffc]dcfe[dRc^\[^QVOZXXZSPFWNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@2971:937/2 +CTCGCACGGCCGCCTCGACCACTTGGTCTGGCGTCATGCGCAATTTTTTCTCCATGTGGAACGGGCTGGTGGCGATGAACGTATGAATATGCCCCCGCGCT ++2971:937/2 +hhhddhefhh_ffffhhhhfah_hhdUdcfW`fbbhfcaec_dfdbba````W^caaaJXGKXSUVYVZY^WY^BBBBBBBBBBBBBBBBBBBBBBBBBBB +@3786:949/2 +CTCAACCAGAACACCGTGATCGGCGACCAGTTGGCGCAGTTCGCCATCAGAAATGCAGGGATGCGGATGCGGGCTAGCACGAAAGTCATCCTCAACACGAT ++3786:949/2 +ffcfcaffff\_edefddff[ffa_fRffRdc]Sdf]affehh_eaebBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@4205:944/2 +GTCGACAGGTGCCTGTACACCACGCCAGGCCAGCCAGGCGAAACCGAGAACGGTCACCATCTGAACCAGACCGAAAACCAACAGTGCGGGGTTGAGCCACG ++4205:944/2 +hhhhhcffcWcdfdcffdffdfQadf[fLfc`Ra`Wcca]`^``]L[^QZGSQWUYZXK[`bJRbZb[_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@4534:934/2 +GGTAATTGCGGACGGCTTCGGCAATTTCGGCCAGGTAGCGCACGCGCTTCGACGGAACGATGGCGCGCAGGTTCGACGATTGTCGAACGCTGATCAGCGCG ++4534:934/2 +ffffcff[fdhaghh[ffcahhghhhdhadhhhhg_hc[hf]fec]faa]bLb___`^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB |
| b |
| diff -r 000000000000 -r f0949bc49926 test-data/paired_end_2_cleaned.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_end_2_cleaned.fastqsanger Mon Jan 27 09:27:16 2014 -0500 |
| [ |
| @@ -0,0 +1,16 @@ +@2971:937/2 +CTCGCACGGCCGCCTCGACCACTTGGTCTGGCGTCATGCGCAATTTTTTCTCCATGTGGAACGGGCTGGTGGCGATGAACGTATGAATATGCCCCCGCGCT ++2971:937/2 +hhhddhefhh_ffffhhhhfah_hhdUdcfW`fbbhfcaec_dfdbba````W^caaaJXGKXSUVYVZY^WY^BBBBBBBBBBBBBBBBBBBBBBBBBBB +@3786:949/2 +CTCAACCAGAACACCGTGATCGGCGACCAGTTGGCGCAGTTCGCCATCAGAAATGCAGGGATGCGGATGCGGGCTAGCACGAAAGTCATCCTCAACACGAT ++3786:949/2 +ffcfcaffff\_edefddff[ffa_fRffRdc]Sdf]affehh_eaebBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@4205:944/2 +GTCGACAGGTGCCTGTACACCACGCCAGGCCAGCCAGGCGAAACCGAGAACGGTCACCATCTGAACCAGACCGAAAACCAACAGTGCGGGGTTGAGCCACG ++4205:944/2 +hhhhhcffcWcdfdcffdffdfQadf[fLfc`Ra`Wcca]`^``]L[^QZGSQWUYZXK[`bJRbZb[_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@4534:934/2 +GGTAATTGCGGACGGCTTCGGCAATTTCGGCCAGGTAGCGCACGCGCTTCGACGGAACGATGGCGCGCAGGTTCGACGATTGTCGAACGCTGATCAGCGCG ++4534:934/2 +ffffcff[fdhaghh[ffcahhghhhdhadhhhhg_hc[hf]fec]faa]bLb___`^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB |
| b |
| diff -r 000000000000 -r f0949bc49926 test-data/paired_end_2_cleaned_singles.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_end_2_cleaned_singles.fastqsanger Mon Jan 27 09:27:16 2014 -0500 |
| [ |
| @@ -0,0 +1,4 @@ +@9999:931/2 +GCGCGTAACGTTTCACCTCGAGATCGTTGTCGGCCGCAATCTCCTGGGGGCGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT ++9999:931/2 +aee_dcadeeWcaaadJbdaff[fffc]dcfe[dRc^\[^QVOZXXZSPFWNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB |
| b |
| diff -r 000000000000 -r f0949bc49926 test-data/paired_end_merged.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_end_merged.fastqsanger Mon Jan 27 09:27:16 2014 -0500 |
| [ |
| @@ -0,0 +1,40 @@ +@1539:931/1 +NACATCAACACTCAGTAACGGCTGGCGCAAAATGGCATTGATTAACGAAGACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG ++1539:931/1 +BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@1539:931/2 this read has a description +GCGCGTAACGTTTCACCTCGAGATCGTTGTCGGCCGCAATCTCCTGGGGGCGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT ++1539:931/2 this read has a description +aee_dcadeeWcaaadJbdaff[fffc]dcfe[dRc^\[^QVOZXXZSPFWNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@2971:937/1 +NCGGAGACTTCGAGGCCATCCAGTCGATTGCCAAAGTCATCAAGGGGTCGACGATCTGCTCCCTTGCCCGTTCCAACGAGAATGAAATCCGCCGCGCGTGG ++2971:937/1 +BMQMMRRRSS__________XXXXXVVVVV_b___Y[Y[YXVRVWWPWVX_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@2971:937/2 +CTCGCACGGCCGCCTCGACCACTTGGTCTGGCGTCATGCGCAATTTTTTCTCCATGTGGAACGGGCTGGTGGCGATGAACGTATGAATATGCCCCCGCGCT ++2971:937/2 +hhhddhefhh_ffffhhhhfah_hhdUdcfW`fbbhfcaec_dfdbba````W^caaaJXGKXSUVYVZY^WY^BBBBBBBBBBBBBBBBBBBBBBBBBBB +@3786:949/1 +NTACCGCGCAACGGCATGATGGCTTGGAACTCACGGTCACGCGCCTGTTTGGCAGAGCCGCCCGCCGAGTCACCTTCCACTAGGAACAGTTCGGAGCGGTT ++3786:949/1 +BKGGKKJNJJ_______W__Y__W_TVPVP[YY[[_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@3786:949/2 +CTCAACCAGAACACCGTGATCGGCGACCAGTTGGCGCAGTTCGCCATCAGAAATGCAGGGATGCGGATGCGGGCTAGCACGAAAGTCATCCTCAACACGAT ++3786:949/2 +ffcfcaffff\_edefddff[ffa_fRffRdc]Sdf]affehh_eaebBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@4205:944/1 +NGATCTGGGCTTCAGCAAGACCGATGTCGGCGTGATTGCCAAGCATGCCGGACTCTGGCCGGCGGGGTTCGGCGGTGTGCTGGGTGGCTTGGGGGTGGGGG ++4205:944/1 +BLLLLTWTTR_V_______TYYYRYYYYYY____VWRWWW___BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@4205:944/2 +GTCGACAGGTGCCTGTACACCACGCCAGGCCAGCCAGGCGAAACCGAGAACGGTCACCATCTGAACCAGACCGAAAACCAACAGTGCGGGGTTGAGCCACG ++4205:944/2 +hhhhhcffcWcdfdcffdffdfQadf[fLfc`Ra`Wcca]`^``]L[^QZGSQWUYZXK[`bJRbZb[_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@4534:934/1 +NAATGCCGGTATTTGGCACGATGGCGGCACGCTTCCACGACGACGGGGTGACCTCTCTCTATCAGGCGATGGCATCCAAATTGCACGCGCGGGGTTTGAGG ++4534:934/1 +BGGFGLJLJL______________V____________________YYYPQOTWVT__________BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@4534:934/2 +GGTAATTGCGGACGGCTTCGGCAATTTCGGCCAGGTAGCGCACGCGCTTCGACGGAACGATGGCGCGCAGGTTCGACGATTGTCGAACGCTGATCAGCGCG ++4534:934/2 +ffffcff[fdhaghh[ffcahhghhhdhadhhhhg_hc[hf]fec]faa]bLb___`^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB |
| b |
| diff -r 000000000000 -r f0949bc49926 test-data/paired_end_merged_errors.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_end_merged_errors.fastqsanger Mon Jan 27 09:27:16 2014 -0500 |
| [ |
| @@ -0,0 +1,40 @@ +@1539:931/1 +NACATCAACACTCAGTAACGGCTGGCGCAAAATGGCATTGATTAACGAAGACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG ++1539:931/1 +BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@9999:931/2 +GCGCGTAACGTTTCACCTCGAGATCGTTGTCGGCCGCAATCTCCTGGGGGCGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT ++9999:931/2 +aee_dcadeeWcaaadJbdaff[fffc]dcfe[dRc^\[^QVOZXXZSPFWNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@2971:937/2 +CTCGCACGGCCGCCTCGACCACTTGGTCTGGCGTCATGCGCAATTTTTTCTCCATGTGGAACGGGCTGGTGGCGATGAACGTATGAATATGCCCCCGCGCT ++2971:937/2 +hhhddhefhh_ffffhhhhfah_hhdUdcfW`fbbhfcaec_dfdbba````W^caaaJXGKXSUVYVZY^WY^BBBBBBBBBBBBBBBBBBBBBBBBBBB +@2971:937/1 +NCGGAGACTTCGAGGCCATCCAGTCGATTGCCAAAGTCATCAAGGGGTCGACGATCTGCTCCCTTGCCCGTTCCAACGAGAATGAAATCCGCCGCGCGTGG ++2971:937/1 +BMQMMRRRSS__________XXXXXVVVVV_b___Y[Y[YXVRVWWPWVX_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@3786:949/1 +NTACCGCGCAACGGCATGATGGCTTGGAACTCACGGTCACGCGCCTGTTTGGCAGAGCCGCCCGCCGAGTCACCTTCCACTAGGAACAGTTCGGAGCGGTT ++3786:949/1 +BKGGKKJNJJ_______W__Y__W_TVPVP[YY[[_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@3786:949/2 +CTCAACCAGAACACCGTGATCGGCGACCAGTTGGCGCAGTTCGCCATCAGAAATGCAGGGATGCGGATGCGGGCTAGCACGAAAGTCATCCTCAACACGAT ++3786:949/2 +ffcfcaffff\_edefddff[ffa_fRffRdc]Sdf]affehh_eaebBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@4205:944/1 +NGATCTGGGCTTCAGCAAGACCGATGTCGGCGTGATTGCCAAGCATGCCGGACTCTGGCCGGCGGGGTTCGGCGGTGTGCTGGGTGGCTTGGGGGTGGGGG ++4205:944/1 +BLLLLTWTTR_V_______TYYYRYYYYYY____VWRWWW___BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@4205:944/2 +GTCGACAGGTGCCTGTACACCACGCCAGGCCAGCCAGGCGAAACCGAGAACGGTCACCATCTGAACCAGACCGAAAACCAACAGTGCGGGGTTGAGCCACG ++4205:944/2 +hhhhhcffcWcdfdcffdffdfQadf[fLfc`Ra`Wcca]`^``]L[^QZGSQWUYZXK[`bJRbZb[_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@4534:934/1 +NAATGCCGGTATTTGGCACGATGGCGGCACGCTTCCACGACGACGGGGTGACCTCTCTCTATCAGGCGATGGCATCCAAATTGCACGCGCGGGGTTTGAGG ++4534:934/1 +BGGFGLJLJL______________V____________________YYYPQOTWVT__________BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@4534:934/2 +GGTAATTGCGGACGGCTTCGGCAATTTCGGCCAGGTAGCGCACGCGCTTCGACGGAACGATGGCGCGCAGGTTCGACGATTGTCGAACGCTGATCAGCGCG ++4534:934/2 +ffffcff[fdhaghh[ffcahhghhhdhadhhhhg_hc[hf]fec]faa]bLb___`^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB |
| b |
| diff -r 000000000000 -r f0949bc49926 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jan 27 09:27:16 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> |