Mercurial > repos > mvdbeek > generate_sliding_windows
changeset 0:559cf4ca1f2d draft
Uploaded
| author | mvdbeek |
|---|---|
| date | Wed, 15 Apr 2015 06:34:23 -0400 |
| parents | |
| children | 10a0153b74d1 |
| files | generate_sliding_windows.py generate_sliding_windows.xml test-data/EcR_USP_224.fa test-data/output.fa tool_dependencies.xml |
| diffstat | 5 files changed, 787 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate_sliding_windows.py Wed Apr 15 06:34:23 2015 -0400 @@ -0,0 +1,68 @@ +#!/usr/bin/env python +from Bio import SeqIO +import argparse +import sys + +def generate_windows(seq, window, step): + ''' + Generates windows of a sequence, with the distance of windows + defined by *step*. + + seq -- string to split into windows. + window -- integer specifying the size the generated fragments. + step -- integer specifiying the distance between adjacent fragments. + ''' + stop = window + end = len(seq) + for i in range(stop, end, step): + start = stop-window + fragment = seq[start:stop] + stop_coordinate = stop #to return real stop coordinate + stop = stop+step + yield (fragment, start+1, stop_coordinate) #start+1 to adjust 0-based range + + +def write_fragment(description, output_handle, fragment, start, stop): + '''Write out fragments as fasta with description and start/stop coordinates as fasta header''' + output_string = ">{0}_start:{1}_stop:{2}\n{3}\n".format(description, start, stop, fragment) + output_handle.write(output_string) + + +def handle_io(input, output, window = 21, step= 21): + ''' + Keyword arguments: + input -- file handle for fasta file containing sequences for which you wish to generate fragments. + output -- file handle for the multi-fasta that will contain the generated fragments. + window -- integer specifying the size of the fragments. + step -- integer specifiying the distance between adjacent fragments. + ''' + record_iterator = SeqIO.parse(input, "fasta") + for entry in record_iterator: + seq = str(entry.seq) + description = str(entry.description) + windows = generate_windows(seq, window, step) + [write_fragment(description, output, *fragment) for fragment in windows] + output.close() + input.close() + +def positive_int(val): + try: + assert(int(val) > 0) + except: + raise ArgumentTypeError("'%s' is not a valid positive int" % val) + return int(val) + +if __name__ == "__main__": + + parser = argparse.ArgumentParser(description='Generate fixed size windows in fasta format from multi-fasta sequence.') + parser.add_argument('--input', type=argparse.FileType('r'), required=True, + help='supply an input multi-fasta file.') + parser.add_argument('--output', type=argparse.FileType('w'), default=sys.stdout, + help='supply an output multi-fasta file. If not specified use stdout.') + parser.add_argument('--window', type=positive_int, default=21, + help='Set the size of the generated windows') + parser.add_argument('--step', type=positive_int, default=21, + help='Set distance between the windows') + args = parser.parse_args() + + handle_io(args.input, args.output, args.window, args.step)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate_sliding_windows.xml Wed Apr 15 06:34:23 2015 -0400 @@ -0,0 +1,42 @@ +<tool id="generate_sliding_windows" name="generate_sliding_windows" version="0.1.1"> +<description>"Split fasta sequence in nucleotide windows"</description> + <requirements> + <requirement type="package" version="1.65">biopython</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + + <command interpreter="python"><![CDATA[ + generate_sliding_windows.py --input "$input1" --output "$output1" --window $window --step $step + ]]></command> + <inputs> + <param type="data" name="input" label="input fasta file" help="select fasta file for which you wish to generate a multi-fasta file in a sliding window fashion" format="fasta" /> + <param type="integer" name="window" value="21" min="1" label="window size" help="Specifiy the size of the windows that should be generated"/> + <param type="integer" name="step" value="21" min="1" label="step size" help="Specify the distance with which windows should be spaced apart."/> + </inputs> + <outputs> + <data name="output1" format="fasta" /> + </outputs> + <tests> + <test> + <param name="input1" value="EcR_USP_224.fa"/> + <param name="window" value="21"/> + <param name="step" value="21"/> + <output name="output1" file="output.fa"/> + </test> + </tests> + <help><![CDATA[ + +Generate fixed size sliding windows in fasta format from multi-fasta sequence. + +optional arguments: + -h, --help show this help message and exit + --input INPUT supply an input multi-fasta file. + --output OUTPUT supply an output multi-fasta file. If not specified use + stdout. + --window WINDOW Set the size of the generated windows + --step STEP Set distance between the windows + + ]]></help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/EcR_USP_224.fa Wed Apr 15 06:34:23 2015 -0400 @@ -0,0 +1,101 @@ +>3L:3245372,3251371 +AGGAGGCTATGTTTCTTAATGATGAACTGGTATATTATATTTTCGAAACTTTCATTTAAT +GTAAAAACACTGTTATTAGTAAATGGAATCTTCCATAACAGGGTCCACCCCAATCGATCA +TCCCACTCATTAGGTTTCTTCCTCGTCTGAGAGGACCAGAGGTCCCGAGGCTTGCGTTTT +TGCGGTGACTGTGGCGTCTGCTGGGTGTCAACATTTAGCCGCATGTTGTGCGGCTGCCAC +AACTGCAGTTCCCCAATTCTGGATAAAAAAAAAAAAACGCCGTCAAACAGAAGGGTGAAA +TTAACTTCGGAGTCGGACGAGGAGGAGTGCTTAGCACCCGCATCCAGGCACATGTGCTGT +TCTTCTCGACATGCGACATTCGTACAGTCGCCGAGTCAATCAGACCGGAAAATATGCACA +AATTCCAATGGCTTTTGTCATGTTGCAAGGCGATTGTGACTACATTTTTGCCATTTCTAT +TTCCCAAATAGCGGCTAAAACAGTTGTGGCCATTAACTTAGTGCTATGAATGTAGTTACT +GTTCTTGTGAATTGCTTAATTTCCCTTTCAATCATCTAAAATAAATAAATACAAATGAAT +GAACCAAAGTCATTACCCTGCCTAAAACACATTTTCTTCCCTTAGAACTTTGTACCCCTT +TTATATTTCGAATTGCAAATGGAAGGGTGAAATTAGCGGCAAGTGGAGCTATTTTCCGCG +CGGTGTATGGTTATCACAACGCTTATCTCACTACGCGATTGTCGGAACCTGTAAACGCGA +TTTTGTCAGCCAGGTTTTTTTGGCTGCCAGCACTTGACGTGTGTTAAATTAGCATTAAAC +AATAATTTTGTGCCTGTTTTTCTTTTTTTGGCTTTGCCGCTGTTGTTGTTGCTGTTACTG +TTGTGGTGAATGCAAAATAAATTGCGCATAAAGTTTAATCACTTTGACTTTGCACAACAC +ACACGCACGCACACACACTTGCAATGCCAAAAAATAAAAACGCACAACAAAAGATTCTCC +ACACACAGATACACAGATACTGAATACAATATCGGCAGCAGCAGCGCAAACCAAAACAAC +AACGACGAGCCCAGTGGACAGTGCAAAATAAGTATAAAAATAAATAAGAAAAATTAAAAA +AAAAGGAAATAAATAAAAAAATACACAAGGCGAAGGCGACGATGGCAACAGGCAGAGCGA +GCGGGATGCAAATAGAGTCAACAACCTCCAGTGCATTACTCACTTTTAAAGACCGTGTCT +GTCCTTCAACGAAAACTTTATCTCTGTCCCTCACTCGCTCGCTCTGCATCTGCATCTCAG +CTTTTGCTCCCTCTCTCTCTCGCTCGCTCTCACTCGAGCAGCCCGATTCGTTTTTTACTT +CTTATAATTAAACAATTTTGCAGCGGCACTCCCCCAGCGCCCCCATTTCGTACTCCCCCC +GCCGTCTTCATCTTTTTCCGGACAAACAGAACCCGAAAAAGTGATCTTGCTGCACGGAAA +GAAATCGAATCGTTGTCTAACAATAGAAATGCTGCTTTATAAGGCAACCAATTGAAGTCT +TTCGTTCTTCAAAACCTAATTCAAAGATTAACCACTTTTTTGCTATATCTATCCTTAAGC +TTTAAAATTCGAATAGTAATAGGATTTAACTCTATAGTAGTAGTATCTTATCATATTATC +AGTACGATTTTTCCCAAAGTGCCATTGTTTTTGGTCACTATGGTCTTGTTCTTGTTCCCG +GAGATTTGCACAAGTGTGCAGAAGACAGTCTTCTATCTCCACTTTATCGATGGGGCTTCG +GAAAGTTTGTCGATTCCGCTGCTGCGCATTTTGGCGAGATGCGAGATGAATAAACTGTTG +TACGCTTGCGTGACCTGTTCGCCATCTCGGTTGCTCCTCCTGCGCCCTCTTTTCCTCTCT +CTACCCCCCTCCCCCACGCAAAGGAAAGAGACGGAGCGATTGCCACATCCGCCCTGCATG +TTTGTGCGCTTTTTGTGCGACTAATGTCATTGACTGCAATTTGTTAGCAAAGTATTTCGA +CTGATAAACAAAATCTGCACGATGCCAATGAACCCGGCTCTCTAAAATTGCCATCCGAAA +GCCAAAACAACCCGAAATTGCAATTCGCGCCCCAATTGGAGAGCAACTAGGTAGGCGTGT +GTAACAGAGATAGCAATCGGGCCTTGCACTCACACTCCCTAAGGAGCAGAGGTGGATTCT +AACGGGGATTTGACGGAACGCGAATTCTTTAGCATTCTATATCTGCACCTTATAAGAATT +TCCACTGAGTTCTAAGTTGAGATTTCATAATATTTAGTATTTTAACTATGTTTTTTCGTA +TAAGTTTTGTTATTACTCTGCTATGACTTCCATAACCCCTTTTTAGAAGTGCTTTTCCTT +ATCCGCCTCTGCACATGAGCACAGGTTGGCAATGCCATAAACAAAGAATTCCTTTTGTTT +GTTGATTCGATTTTTGTTCTGCGATCTTTTTATTTCTTTGCAAATTGTATTTTTATTTTT +AAATAAACAAGCCGAGTTCATTGCATTCGCCAGAATAAGAATATAACAAATACGGCACGA +AAAGCACTCGACAACCGACAAAAGGCGCAGAAAAACAGGAACGTCGACTGACATACATGG +CGTATAATTAACGGCTGCGCGTGTAGAGAGAGTTCAAGTTACTTTATCAATTCTTTCTTT +TTCGGGACCTAACAATACTCATACTTGCACTTAAGTAGGCGGAGTGAAAGCCAAGTCATA +ATTTCGACGATGCGTATACATATATAGAATCAATCAACTGATTAATTGCAGCTGTGCAAC +GCTTGAGTTTTTGCCTCAGCCTTTCGTCTGGTGACATAGTTTACTCGATTAATTATGGTA +AGTAATAAGGGTTTAAAATAATTGAAAACCCCAGCACTTGCGTGTATTATATATAACGAT +GATTTAACAGCACCTCCTTTATAAATAAAACCAATCCCTTCAAGTGCGAACAGCTATGTT +TTCCGCTCATCTGGCGCATTTATCAGATGGTGCCATATTTCCTCGGAGAAGAAGGCATTG +AATGTCAGTGGTGTTCGGATTACACTAAAGTCGGTCAATAACTTCGGACCCCTGCACAAA +GCGTTTAAGTGACCACAAGTGATCGAGATGTTCCTCTTGTTGTTTACCCCCTTGCCAACT +GATCTTAAGTTTGGGATGCCACGCTAGTTTAGTTGACCGGTTTAATGACTCGAACTTAAT +TTGCGCCCTCGGAGAGAGGAAAGTAGCCAGCAAAAAATGCAAGCCGAAAAATATGCGAAA +CAACCAGGCAGACAACACCCAACGGCAAAAACTCGGCCTGGAGAGAAAGAGGCAGTGGCA +GCGACGCGTCTGGGGGCTTACAATGGCGGTCGCAACACTAGTGGCGCTTGTAAATAGAGA +CATAACGAAAAGGTATTAAAAATGATGCGGCAAAAGAAATAACTGCACTATTTTCCATAA +AAATATTTTGAAAAATAAACTGTTGCGCCGTTTTTAGAGATCTTAAAAACCTCTTTACGT +CAACTTTGATAACTAATTGAGTTCCTTTGCATAGTTATGATTTTTAAAAATAACAATTTA +AGATACATGATATTCCCTACATGAACAATTAGTGGTTTATAATAAATAAGCAACCTAATG +CGTAAGATCCCACAATCTTGACCGCTACTGTGAAAAGGGGGGGATCTGCGTGAGTGTGCG +TGTATGTGGGGAGAGGGCTGCAGTGGGCGGGGCAGGCTGCAGGAAGAGCCCCCAGGCGAG +CGTGTGTATGTGAGTGGGTCGCCAAAACAGACAAAAAACGAGGAGTGCATACGAGCAGAA +GCAGCAGTGCTGCCCCAAAAGAACGATGCTCGAACCGAAAGTAACTCATATTCGCGGCTG +CGAGAGTGTGTGCGTGTGCGGCGACGGATCAGGCAAATATATAAAGCGGCGATCGGGCAA +TGCAAACTGCTCATTCCGTCGCCGTTCGTTCCGTTCGCTTTACTTTTCGTACTTTTCTCG +CATATTAAAAAGTCAAACAAAATAATAAAATGAAGCGATCGCACACATACTCACGCACAT +ACGTGTATATGTTCGTACATATATATATGTACATATGCATACATATATATGCACGCAATG +GCCGCCATTGACGCCGACTGCGCTGCCGACTGCGCTGGCGAGAGTATAAAAGCATAAAAT +CACTTCGTACTCGGGTTTATTAAAACCAAAACTGTGCAAGTGTCAAGATCGGTTAGCAGC +AGCAAAAAGATAAATAAGAAATAGCCAAGGACCCATAAAATAAATAATCTCAATACCAAA +AAGTTCTAGTGAAATTCACAATTCTGACTTGGAAAGTGAAAGTTTGGCCATTAAACGTAC +GATTAAAATCCACAACAGCACGATCAAAAATAGTATCAAGCAATTAGCGCAGAAAAAGTA +ACAAAAAAAATTTTAAAAAACAGGAACGCGACGTGCCCGCAAAAGCGAAAAAAAATTAAA +ATCGAAAGTGTTCTACTGACATGGATTACTTTTTGCCGCCCAAACTACAAACACAACAAA +ACGCGCAGAGAAACTAGCACTACTTTTTTCTATTCACCCATTCGGAGAGTGAGAAGAATC +GGAGAGAAGGAAAGAGAGCAAAGGCCGGTCCGAAATAGAAAGCACTACACTGGAAAATCT +GTTAATAAGAATGCAATGAAAGTAATACGAAACACAGATATATTTAGCTTATATTACTCT +TAAAACTCTAGAAAAATCTAGATCGGTTAATATAACAATTTTAAAATAGCTTAGTTGGCA +TCGATGTTACGGAAAAAATTTTTCCAGTTGTACTTGAAAGGCAGAAATATTTCGAGATTT +AGATTTATGAGTCTTCCTAAAGAAATTAAATTGGATAGAAAATGTCTTTTAGATATAGAA +TACAGGGTGATGCCTAATCCATTAAAATCGAGCAATCTAAAAAGTGTCATACCAGTTAGA +TTGGGTGTAACCAACGCAACGTTCTCACTGTGTAGATAGCGATCTCTTCTATTCGGCGGT +GTACGTGCACTTGGCCATTTGTCTCTCCATTCTCCATTTTTCGCGCCTCGCTCTCAATTC +TCTGCGCTCAAATCCTCTAGCAATTCTAATTCGTATTCTCGCCGCCTCGCTTTGAACTTG +AACTTTAAATGCACAAACCATAATCGTGTATGTTATGTTGTTGCTGGCCGAGGGCGTGCT +CTCGCACTCTGGCAAACATGGGCTCTACGAGTTTGCTATATATACGCAGCGCAATCAGTT +GCGAGGCAGCACTCGTTCCATGTGGGCGCTCGACAATCGCCCGCTGATCAGTTTTCGACT +GGCTTGCAATTAATTCGGCTCTTGACGAGCCCCAAAAGTGAAAGTCGCGAGTGAAAGACG +TGGCAGTTTTATATTAAAGAAAAATACGAAAACGGGCAGCAGATCAAACATGAACAGTAC +GCAAAACACGAAATGCGAAACGGCGGCAACAAGTTAATAAATTAAGACGGCAAACGAAAA +AATCCAGATTCCGAGCACTGCAAAGAAAGTGGCACAAATGCTTTGCTTTTATCGTAGGAA +ATTCGCAAAAAATGTACAAATAAAACGAAAGAAAAGTTGCCACTATCAAATCCCACCGTT +CTTTAACTATAGTTTCCTTCTAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTCGAAA +GCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCGAACAATCAGCGAAAACG +GAATCGATTACAGTTTTGGAGATCGTGAGAGGAGGAGAAGAGGCGACTGCTTGATAAGCC +CGGACCCTCCAGCGATCTCCAATCAATATTACTTTCCACCTACATATCTCCCCCTTTCAG +CTGGTTTAATTTTGGATTCCCCCATCTGGCTGGCCTATTTTCGCCTGGCCTGCGTTATTT +ATTAGTTAATAAACCATTAATATATACTTGAATAAAAAGGCGTTTCTCTGATTTTTGATG \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.fa Wed Apr 15 06:34:23 2015 -0400 @@ -0,0 +1,570 @@ +>3L:3245372,3251371_start:1_stop:21 +AGGAGGCTATGTTTCTTAATG +>3L:3245372,3251371_start:22_stop:42 +ATGAACTGGTATATTATATTT +>3L:3245372,3251371_start:43_stop:63 +TCGAAACTTTCATTTAATGTA +>3L:3245372,3251371_start:64_stop:84 +AAAACACTGTTATTAGTAAAT +>3L:3245372,3251371_start:85_stop:105 +GGAATCTTCCATAACAGGGTC +>3L:3245372,3251371_start:106_stop:126 +CACCCCAATCGATCATCCCAC +>3L:3245372,3251371_start:127_stop:147 +TCATTAGGTTTCTTCCTCGTC +>3L:3245372,3251371_start:148_stop:168 +TGAGAGGACCAGAGGTCCCGA +>3L:3245372,3251371_start:169_stop:189 +GGCTTGCGTTTTTGCGGTGAC +>3L:3245372,3251371_start:190_stop:210 +TGTGGCGTCTGCTGGGTGTCA +>3L:3245372,3251371_start:211_stop:231 +ACATTTAGCCGCATGTTGTGC +>3L:3245372,3251371_start:232_stop:252 +GGCTGCCACAACTGCAGTTCC +>3L:3245372,3251371_start:253_stop:273 +CCAATTCTGGATAAAAAAAAA +>3L:3245372,3251371_start:274_stop:294 +AAAACGCCGTCAAACAGAAGG +>3L:3245372,3251371_start:295_stop:315 +GTGAAATTAACTTCGGAGTCG +>3L:3245372,3251371_start:316_stop:336 +GACGAGGAGGAGTGCTTAGCA +>3L:3245372,3251371_start:337_stop:357 +CCCGCATCCAGGCACATGTGC +>3L:3245372,3251371_start:358_stop:378 +TGTTCTTCTCGACATGCGACA +>3L:3245372,3251371_start:379_stop:399 +TTCGTACAGTCGCCGAGTCAA +>3L:3245372,3251371_start:400_stop:420 +TCAGACCGGAAAATATGCACA +>3L:3245372,3251371_start:421_stop:441 +AATTCCAATGGCTTTTGTCAT +>3L:3245372,3251371_start:442_stop:462 +GTTGCAAGGCGATTGTGACTA +>3L:3245372,3251371_start:463_stop:483 +CATTTTTGCCATTTCTATTTC +>3L:3245372,3251371_start:484_stop:504 +CCAAATAGCGGCTAAAACAGT +>3L:3245372,3251371_start:505_stop:525 +TGTGGCCATTAACTTAGTGCT +>3L:3245372,3251371_start:526_stop:546 +ATGAATGTAGTTACTGTTCTT +>3L:3245372,3251371_start:547_stop:567 +GTGAATTGCTTAATTTCCCTT +>3L:3245372,3251371_start:568_stop:588 +TCAATCATCTAAAATAAATAA +>3L:3245372,3251371_start:589_stop:609 +ATACAAATGAATGAACCAAAG +>3L:3245372,3251371_start:610_stop:630 +TCATTACCCTGCCTAAAACAC +>3L:3245372,3251371_start:631_stop:651 +ATTTTCTTCCCTTAGAACTTT +>3L:3245372,3251371_start:652_stop:672 +GTACCCCTTTTATATTTCGAA +>3L:3245372,3251371_start:673_stop:693 +TTGCAAATGGAAGGGTGAAAT +>3L:3245372,3251371_start:694_stop:714 +TAGCGGCAAGTGGAGCTATTT +>3L:3245372,3251371_start:715_stop:735 +TCCGCGCGGTGTATGGTTATC +>3L:3245372,3251371_start:736_stop:756 +ACAACGCTTATCTCACTACGC +>3L:3245372,3251371_start:757_stop:777 +GATTGTCGGAACCTGTAAACG +>3L:3245372,3251371_start:778_stop:798 +CGATTTTGTCAGCCAGGTTTT +>3L:3245372,3251371_start:799_stop:819 +TTTGGCTGCCAGCACTTGACG +>3L:3245372,3251371_start:820_stop:840 +TGTGTTAAATTAGCATTAAAC +>3L:3245372,3251371_start:841_stop:861 +AATAATTTTGTGCCTGTTTTT +>3L:3245372,3251371_start:862_stop:882 +CTTTTTTTGGCTTTGCCGCTG +>3L:3245372,3251371_start:883_stop:903 +TTGTTGTTGCTGTTACTGTTG +>3L:3245372,3251371_start:904_stop:924 +TGGTGAATGCAAAATAAATTG +>3L:3245372,3251371_start:925_stop:945 +CGCATAAAGTTTAATCACTTT +>3L:3245372,3251371_start:946_stop:966 +GACTTTGCACAACACACACGC +>3L:3245372,3251371_start:967_stop:987 +ACGCACACACACTTGCAATGC +>3L:3245372,3251371_start:988_stop:1008 +CAAAAAATAAAAACGCACAAC +>3L:3245372,3251371_start:1009_stop:1029 +AAAAGATTCTCCACACACAGA +>3L:3245372,3251371_start:1030_stop:1050 +TACACAGATACTGAATACAAT +>3L:3245372,3251371_start:1051_stop:1071 +ATCGGCAGCAGCAGCGCAAAC +>3L:3245372,3251371_start:1072_stop:1092 +CAAAACAACAACGACGAGCCC +>3L:3245372,3251371_start:1093_stop:1113 +AGTGGACAGTGCAAAATAAGT +>3L:3245372,3251371_start:1114_stop:1134 +ATAAAAATAAATAAGAAAAAT +>3L:3245372,3251371_start:1135_stop:1155 +TAAAAAAAAAGGAAATAAATA +>3L:3245372,3251371_start:1156_stop:1176 +AAAAAATACACAAGGCGAAGG +>3L:3245372,3251371_start:1177_stop:1197 +CGACGATGGCAACAGGCAGAG +>3L:3245372,3251371_start:1198_stop:1218 +CGAGCGGGATGCAAATAGAGT +>3L:3245372,3251371_start:1219_stop:1239 +CAACAACCTCCAGTGCATTAC +>3L:3245372,3251371_start:1240_stop:1260 +TCACTTTTAAAGACCGTGTCT +>3L:3245372,3251371_start:1261_stop:1281 +GTCCTTCAACGAAAACTTTAT +>3L:3245372,3251371_start:1282_stop:1302 +CTCTGTCCCTCACTCGCTCGC +>3L:3245372,3251371_start:1303_stop:1323 +TCTGCATCTGCATCTCAGCTT +>3L:3245372,3251371_start:1324_stop:1344 +TTGCTCCCTCTCTCTCTCGCT +>3L:3245372,3251371_start:1345_stop:1365 +CGCTCTCACTCGAGCAGCCCG +>3L:3245372,3251371_start:1366_stop:1386 +ATTCGTTTTTTACTTCTTATA +>3L:3245372,3251371_start:1387_stop:1407 +ATTAAACAATTTTGCAGCGGC +>3L:3245372,3251371_start:1408_stop:1428 +ACTCCCCCAGCGCCCCCATTT +>3L:3245372,3251371_start:1429_stop:1449 +CGTACTCCCCCCGCCGTCTTC +>3L:3245372,3251371_start:1450_stop:1470 +ATCTTTTTCCGGACAAACAGA +>3L:3245372,3251371_start:1471_stop:1491 +ACCCGAAAAAGTGATCTTGCT +>3L:3245372,3251371_start:1492_stop:1512 +GCACGGAAAGAAATCGAATCG +>3L:3245372,3251371_start:1513_stop:1533 +TTGTCTAACAATAGAAATGCT +>3L:3245372,3251371_start:1534_stop:1554 +GCTTTATAAGGCAACCAATTG +>3L:3245372,3251371_start:1555_stop:1575 +AAGTCTTTCGTTCTTCAAAAC +>3L:3245372,3251371_start:1576_stop:1596 +CTAATTCAAAGATTAACCACT +>3L:3245372,3251371_start:1597_stop:1617 +TTTTTGCTATATCTATCCTTA +>3L:3245372,3251371_start:1618_stop:1638 +AGCTTTAAAATTCGAATAGTA +>3L:3245372,3251371_start:1639_stop:1659 +ATAGGATTTAACTCTATAGTA +>3L:3245372,3251371_start:1660_stop:1680 +GTAGTATCTTATCATATTATC +>3L:3245372,3251371_start:1681_stop:1701 +AGTACGATTTTTCCCAAAGTG +>3L:3245372,3251371_start:1702_stop:1722 +CCATTGTTTTTGGTCACTATG +>3L:3245372,3251371_start:1723_stop:1743 +GTCTTGTTCTTGTTCCCGGAG +>3L:3245372,3251371_start:1744_stop:1764 +ATTTGCACAAGTGTGCAGAAG +>3L:3245372,3251371_start:1765_stop:1785 +ACAGTCTTCTATCTCCACTTT +>3L:3245372,3251371_start:1786_stop:1806 +ATCGATGGGGCTTCGGAAAGT +>3L:3245372,3251371_start:1807_stop:1827 +TTGTCGATTCCGCTGCTGCGC +>3L:3245372,3251371_start:1828_stop:1848 +ATTTTGGCGAGATGCGAGATG +>3L:3245372,3251371_start:1849_stop:1869 +AATAAACTGTTGTACGCTTGC +>3L:3245372,3251371_start:1870_stop:1890 +GTGACCTGTTCGCCATCTCGG +>3L:3245372,3251371_start:1891_stop:1911 +TTGCTCCTCCTGCGCCCTCTT +>3L:3245372,3251371_start:1912_stop:1932 +TTCCTCTCTCTACCCCCCTCC +>3L:3245372,3251371_start:1933_stop:1953 +CCCACGCAAAGGAAAGAGACG +>3L:3245372,3251371_start:1954_stop:1974 +GAGCGATTGCCACATCCGCCC +>3L:3245372,3251371_start:1975_stop:1995 +TGCATGTTTGTGCGCTTTTTG +>3L:3245372,3251371_start:1996_stop:2016 +TGCGACTAATGTCATTGACTG +>3L:3245372,3251371_start:2017_stop:2037 +CAATTTGTTAGCAAAGTATTT +>3L:3245372,3251371_start:2038_stop:2058 +CGACTGATAAACAAAATCTGC +>3L:3245372,3251371_start:2059_stop:2079 +ACGATGCCAATGAACCCGGCT +>3L:3245372,3251371_start:2080_stop:2100 +CTCTAAAATTGCCATCCGAAA +>3L:3245372,3251371_start:2101_stop:2121 +GCCAAAACAACCCGAAATTGC +>3L:3245372,3251371_start:2122_stop:2142 +AATTCGCGCCCCAATTGGAGA +>3L:3245372,3251371_start:2143_stop:2163 +GCAACTAGGTAGGCGTGTGTA +>3L:3245372,3251371_start:2164_stop:2184 +ACAGAGATAGCAATCGGGCCT +>3L:3245372,3251371_start:2185_stop:2205 +TGCACTCACACTCCCTAAGGA +>3L:3245372,3251371_start:2206_stop:2226 +GCAGAGGTGGATTCTAACGGG +>3L:3245372,3251371_start:2227_stop:2247 +GATTTGACGGAACGCGAATTC +>3L:3245372,3251371_start:2248_stop:2268 +TTTAGCATTCTATATCTGCAC +>3L:3245372,3251371_start:2269_stop:2289 +CTTATAAGAATTTCCACTGAG +>3L:3245372,3251371_start:2290_stop:2310 +TTCTAAGTTGAGATTTCATAA +>3L:3245372,3251371_start:2311_stop:2331 +TATTTAGTATTTTAACTATGT +>3L:3245372,3251371_start:2332_stop:2352 +TTTTTCGTATAAGTTTTGTTA +>3L:3245372,3251371_start:2353_stop:2373 +TTACTCTGCTATGACTTCCAT +>3L:3245372,3251371_start:2374_stop:2394 +AACCCCTTTTTAGAAGTGCTT +>3L:3245372,3251371_start:2395_stop:2415 +TTCCTTATCCGCCTCTGCACA +>3L:3245372,3251371_start:2416_stop:2436 +TGAGCACAGGTTGGCAATGCC +>3L:3245372,3251371_start:2437_stop:2457 +ATAAACAAAGAATTCCTTTTG +>3L:3245372,3251371_start:2458_stop:2478 +TTTGTTGATTCGATTTTTGTT +>3L:3245372,3251371_start:2479_stop:2499 +CTGCGATCTTTTTATTTCTTT +>3L:3245372,3251371_start:2500_stop:2520 +GCAAATTGTATTTTTATTTTT +>3L:3245372,3251371_start:2521_stop:2541 +AAATAAACAAGCCGAGTTCAT +>3L:3245372,3251371_start:2542_stop:2562 +TGCATTCGCCAGAATAAGAAT +>3L:3245372,3251371_start:2563_stop:2583 +ATAACAAATACGGCACGAAAA +>3L:3245372,3251371_start:2584_stop:2604 +GCACTCGACAACCGACAAAAG +>3L:3245372,3251371_start:2605_stop:2625 +GCGCAGAAAAACAGGAACGTC +>3L:3245372,3251371_start:2626_stop:2646 +GACTGACATACATGGCGTATA +>3L:3245372,3251371_start:2647_stop:2667 +ATTAACGGCTGCGCGTGTAGA +>3L:3245372,3251371_start:2668_stop:2688 +GAGAGTTCAAGTTACTTTATC +>3L:3245372,3251371_start:2689_stop:2709 +AATTCTTTCTTTTTCGGGACC +>3L:3245372,3251371_start:2710_stop:2730 +TAACAATACTCATACTTGCAC +>3L:3245372,3251371_start:2731_stop:2751 +TTAAGTAGGCGGAGTGAAAGC +>3L:3245372,3251371_start:2752_stop:2772 +CAAGTCATAATTTCGACGATG +>3L:3245372,3251371_start:2773_stop:2793 +CGTATACATATATAGAATCAA +>3L:3245372,3251371_start:2794_stop:2814 +TCAACTGATTAATTGCAGCTG +>3L:3245372,3251371_start:2815_stop:2835 +TGCAACGCTTGAGTTTTTGCC +>3L:3245372,3251371_start:2836_stop:2856 +TCAGCCTTTCGTCTGGTGACA +>3L:3245372,3251371_start:2857_stop:2877 +TAGTTTACTCGATTAATTATG +>3L:3245372,3251371_start:2878_stop:2898 +GTAAGTAATAAGGGTTTAAAA +>3L:3245372,3251371_start:2899_stop:2919 +TAATTGAAAACCCCAGCACTT +>3L:3245372,3251371_start:2920_stop:2940 +GCGTGTATTATATATAACGAT +>3L:3245372,3251371_start:2941_stop:2961 +GATTTAACAGCACCTCCTTTA +>3L:3245372,3251371_start:2962_stop:2982 +TAAATAAAACCAATCCCTTCA +>3L:3245372,3251371_start:2983_stop:3003 +AGTGCGAACAGCTATGTTTTC +>3L:3245372,3251371_start:3004_stop:3024 +CGCTCATCTGGCGCATTTATC +>3L:3245372,3251371_start:3025_stop:3045 +AGATGGTGCCATATTTCCTCG +>3L:3245372,3251371_start:3046_stop:3066 +GAGAAGAAGGCATTGAATGTC +>3L:3245372,3251371_start:3067_stop:3087 +AGTGGTGTTCGGATTACACTA +>3L:3245372,3251371_start:3088_stop:3108 +AAGTCGGTCAATAACTTCGGA +>3L:3245372,3251371_start:3109_stop:3129 +CCCCTGCACAAAGCGTTTAAG +>3L:3245372,3251371_start:3130_stop:3150 +TGACCACAAGTGATCGAGATG +>3L:3245372,3251371_start:3151_stop:3171 +TTCCTCTTGTTGTTTACCCCC +>3L:3245372,3251371_start:3172_stop:3192 +TTGCCAACTGATCTTAAGTTT +>3L:3245372,3251371_start:3193_stop:3213 +GGGATGCCACGCTAGTTTAGT +>3L:3245372,3251371_start:3214_stop:3234 +TGACCGGTTTAATGACTCGAA +>3L:3245372,3251371_start:3235_stop:3255 +CTTAATTTGCGCCCTCGGAGA +>3L:3245372,3251371_start:3256_stop:3276 +GAGGAAAGTAGCCAGCAAAAA +>3L:3245372,3251371_start:3277_stop:3297 +ATGCAAGCCGAAAAATATGCG +>3L:3245372,3251371_start:3298_stop:3318 +AAACAACCAGGCAGACAACAC +>3L:3245372,3251371_start:3319_stop:3339 +CCAACGGCAAAAACTCGGCCT +>3L:3245372,3251371_start:3340_stop:3360 +GGAGAGAAAGAGGCAGTGGCA +>3L:3245372,3251371_start:3361_stop:3381 +GCGACGCGTCTGGGGGCTTAC +>3L:3245372,3251371_start:3382_stop:3402 +AATGGCGGTCGCAACACTAGT +>3L:3245372,3251371_start:3403_stop:3423 +GGCGCTTGTAAATAGAGACAT +>3L:3245372,3251371_start:3424_stop:3444 +AACGAAAAGGTATTAAAAATG +>3L:3245372,3251371_start:3445_stop:3465 +ATGCGGCAAAAGAAATAACTG +>3L:3245372,3251371_start:3466_stop:3486 +CACTATTTTCCATAAAAATAT +>3L:3245372,3251371_start:3487_stop:3507 +TTTGAAAAATAAACTGTTGCG +>3L:3245372,3251371_start:3508_stop:3528 +CCGTTTTTAGAGATCTTAAAA +>3L:3245372,3251371_start:3529_stop:3549 +ACCTCTTTACGTCAACTTTGA +>3L:3245372,3251371_start:3550_stop:3570 +TAACTAATTGAGTTCCTTTGC +>3L:3245372,3251371_start:3571_stop:3591 +ATAGTTATGATTTTTAAAAAT +>3L:3245372,3251371_start:3592_stop:3612 +AACAATTTAAGATACATGATA +>3L:3245372,3251371_start:3613_stop:3633 +TTCCCTACATGAACAATTAGT +>3L:3245372,3251371_start:3634_stop:3654 +GGTTTATAATAAATAAGCAAC +>3L:3245372,3251371_start:3655_stop:3675 +CTAATGCGTAAGATCCCACAA +>3L:3245372,3251371_start:3676_stop:3696 +TCTTGACCGCTACTGTGAAAA +>3L:3245372,3251371_start:3697_stop:3717 +GGGGGGGATCTGCGTGAGTGT +>3L:3245372,3251371_start:3718_stop:3738 +GCGTGTATGTGGGGAGAGGGC +>3L:3245372,3251371_start:3739_stop:3759 +TGCAGTGGGCGGGGCAGGCTG +>3L:3245372,3251371_start:3760_stop:3780 +CAGGAAGAGCCCCCAGGCGAG +>3L:3245372,3251371_start:3781_stop:3801 +CGTGTGTATGTGAGTGGGTCG +>3L:3245372,3251371_start:3802_stop:3822 +CCAAAACAGACAAAAAACGAG +>3L:3245372,3251371_start:3823_stop:3843 +GAGTGCATACGAGCAGAAGCA +>3L:3245372,3251371_start:3844_stop:3864 +GCAGTGCTGCCCCAAAAGAAC +>3L:3245372,3251371_start:3865_stop:3885 +GATGCTCGAACCGAAAGTAAC +>3L:3245372,3251371_start:3886_stop:3906 +TCATATTCGCGGCTGCGAGAG +>3L:3245372,3251371_start:3907_stop:3927 +TGTGTGCGTGTGCGGCGACGG +>3L:3245372,3251371_start:3928_stop:3948 +ATCAGGCAAATATATAAAGCG +>3L:3245372,3251371_start:3949_stop:3969 +GCGATCGGGCAATGCAAACTG +>3L:3245372,3251371_start:3970_stop:3990 +CTCATTCCGTCGCCGTTCGTT +>3L:3245372,3251371_start:3991_stop:4011 +CCGTTCGCTTTACTTTTCGTA +>3L:3245372,3251371_start:4012_stop:4032 +CTTTTCTCGCATATTAAAAAG +>3L:3245372,3251371_start:4033_stop:4053 +TCAAACAAAATAATAAAATGA +>3L:3245372,3251371_start:4054_stop:4074 +AGCGATCGCACACATACTCAC +>3L:3245372,3251371_start:4075_stop:4095 +GCACATACGTGTATATGTTCG +>3L:3245372,3251371_start:4096_stop:4116 +TACATATATATATGTACATAT +>3L:3245372,3251371_start:4117_stop:4137 +GCATACATATATATGCACGCA +>3L:3245372,3251371_start:4138_stop:4158 +ATGGCCGCCATTGACGCCGAC +>3L:3245372,3251371_start:4159_stop:4179 +TGCGCTGCCGACTGCGCTGGC +>3L:3245372,3251371_start:4180_stop:4200 +GAGAGTATAAAAGCATAAAAT +>3L:3245372,3251371_start:4201_stop:4221 +CACTTCGTACTCGGGTTTATT +>3L:3245372,3251371_start:4222_stop:4242 +AAAACCAAAACTGTGCAAGTG +>3L:3245372,3251371_start:4243_stop:4263 +TCAAGATCGGTTAGCAGCAGC +>3L:3245372,3251371_start:4264_stop:4284 +AAAAAGATAAATAAGAAATAG +>3L:3245372,3251371_start:4285_stop:4305 +CCAAGGACCCATAAAATAAAT +>3L:3245372,3251371_start:4306_stop:4326 +AATCTCAATACCAAAAAGTTC +>3L:3245372,3251371_start:4327_stop:4347 +TAGTGAAATTCACAATTCTGA +>3L:3245372,3251371_start:4348_stop:4368 +CTTGGAAAGTGAAAGTTTGGC +>3L:3245372,3251371_start:4369_stop:4389 +CATTAAACGTACGATTAAAAT +>3L:3245372,3251371_start:4390_stop:4410 +CCACAACAGCACGATCAAAAA +>3L:3245372,3251371_start:4411_stop:4431 +TAGTATCAAGCAATTAGCGCA +>3L:3245372,3251371_start:4432_stop:4452 +GAAAAAGTAACAAAAAAAATT +>3L:3245372,3251371_start:4453_stop:4473 +TTAAAAAACAGGAACGCGACG +>3L:3245372,3251371_start:4474_stop:4494 +TGCCCGCAAAAGCGAAAAAAA +>3L:3245372,3251371_start:4495_stop:4515 +ATTAAAATCGAAAGTGTTCTA +>3L:3245372,3251371_start:4516_stop:4536 +CTGACATGGATTACTTTTTGC +>3L:3245372,3251371_start:4537_stop:4557 +CGCCCAAACTACAAACACAAC +>3L:3245372,3251371_start:4558_stop:4578 +AAAACGCGCAGAGAAACTAGC +>3L:3245372,3251371_start:4579_stop:4599 +ACTACTTTTTTCTATTCACCC +>3L:3245372,3251371_start:4600_stop:4620 +ATTCGGAGAGTGAGAAGAATC +>3L:3245372,3251371_start:4621_stop:4641 +GGAGAGAAGGAAAGAGAGCAA +>3L:3245372,3251371_start:4642_stop:4662 +AGGCCGGTCCGAAATAGAAAG +>3L:3245372,3251371_start:4663_stop:4683 +CACTACACTGGAAAATCTGTT +>3L:3245372,3251371_start:4684_stop:4704 +AATAAGAATGCAATGAAAGTA +>3L:3245372,3251371_start:4705_stop:4725 +ATACGAAACACAGATATATTT +>3L:3245372,3251371_start:4726_stop:4746 +AGCTTATATTACTCTTAAAAC +>3L:3245372,3251371_start:4747_stop:4767 +TCTAGAAAAATCTAGATCGGT +>3L:3245372,3251371_start:4768_stop:4788 +TAATATAACAATTTTAAAATA +>3L:3245372,3251371_start:4789_stop:4809 +GCTTAGTTGGCATCGATGTTA +>3L:3245372,3251371_start:4810_stop:4830 +CGGAAAAAATTTTTCCAGTTG +>3L:3245372,3251371_start:4831_stop:4851 +TACTTGAAAGGCAGAAATATT +>3L:3245372,3251371_start:4852_stop:4872 +TCGAGATTTAGATTTATGAGT +>3L:3245372,3251371_start:4873_stop:4893 +CTTCCTAAAGAAATTAAATTG +>3L:3245372,3251371_start:4894_stop:4914 +GATAGAAAATGTCTTTTAGAT +>3L:3245372,3251371_start:4915_stop:4935 +ATAGAATACAGGGTGATGCCT +>3L:3245372,3251371_start:4936_stop:4956 +AATCCATTAAAATCGAGCAAT +>3L:3245372,3251371_start:4957_stop:4977 +CTAAAAAGTGTCATACCAGTT +>3L:3245372,3251371_start:4978_stop:4998 +AGATTGGGTGTAACCAACGCA +>3L:3245372,3251371_start:4999_stop:5019 +ACGTTCTCACTGTGTAGATAG +>3L:3245372,3251371_start:5020_stop:5040 +CGATCTCTTCTATTCGGCGGT +>3L:3245372,3251371_start:5041_stop:5061 +GTACGTGCACTTGGCCATTTG +>3L:3245372,3251371_start:5062_stop:5082 +TCTCTCCATTCTCCATTTTTC +>3L:3245372,3251371_start:5083_stop:5103 +GCGCCTCGCTCTCAATTCTCT +>3L:3245372,3251371_start:5104_stop:5124 +GCGCTCAAATCCTCTAGCAAT +>3L:3245372,3251371_start:5125_stop:5145 +TCTAATTCGTATTCTCGCCGC +>3L:3245372,3251371_start:5146_stop:5166 +CTCGCTTTGAACTTGAACTTT +>3L:3245372,3251371_start:5167_stop:5187 +AAATGCACAAACCATAATCGT +>3L:3245372,3251371_start:5188_stop:5208 +GTATGTTATGTTGTTGCTGGC +>3L:3245372,3251371_start:5209_stop:5229 +CGAGGGCGTGCTCTCGCACTC +>3L:3245372,3251371_start:5230_stop:5250 +TGGCAAACATGGGCTCTACGA +>3L:3245372,3251371_start:5251_stop:5271 +GTTTGCTATATATACGCAGCG +>3L:3245372,3251371_start:5272_stop:5292 +CAATCAGTTGCGAGGCAGCAC +>3L:3245372,3251371_start:5293_stop:5313 +TCGTTCCATGTGGGCGCTCGA +>3L:3245372,3251371_start:5314_stop:5334 +CAATCGCCCGCTGATCAGTTT +>3L:3245372,3251371_start:5335_stop:5355 +TCGACTGGCTTGCAATTAATT +>3L:3245372,3251371_start:5356_stop:5376 +CGGCTCTTGACGAGCCCCAAA +>3L:3245372,3251371_start:5377_stop:5397 +AGTGAAAGTCGCGAGTGAAAG +>3L:3245372,3251371_start:5398_stop:5418 +ACGTGGCAGTTTTATATTAAA +>3L:3245372,3251371_start:5419_stop:5439 +GAAAAATACGAAAACGGGCAG +>3L:3245372,3251371_start:5440_stop:5460 +CAGATCAAACATGAACAGTAC +>3L:3245372,3251371_start:5461_stop:5481 +GCAAAACACGAAATGCGAAAC +>3L:3245372,3251371_start:5482_stop:5502 +GGCGGCAACAAGTTAATAAAT +>3L:3245372,3251371_start:5503_stop:5523 +TAAGACGGCAAACGAAAAAAT +>3L:3245372,3251371_start:5524_stop:5544 +CCAGATTCCGAGCACTGCAAA +>3L:3245372,3251371_start:5545_stop:5565 +GAAAGTGGCACAAATGCTTTG +>3L:3245372,3251371_start:5566_stop:5586 +CTTTTATCGTAGGAAATTCGC +>3L:3245372,3251371_start:5587_stop:5607 +AAAAAATGTACAAATAAAACG +>3L:3245372,3251371_start:5608_stop:5628 +AAAGAAAAGTTGCCACTATCA +>3L:3245372,3251371_start:5629_stop:5649 +AATCCCACCGTTCTTTAACTA +>3L:3245372,3251371_start:5650_stop:5670 +TAGTTTCCTTCTAAATCTAGC +>3L:3245372,3251371_start:5671_stop:5691 +CTCTACTAGGCTTTGTCTGTG +>3L:3245372,3251371_start:5692_stop:5712 +CATTCGAAAGCCGATCAGACA +>3L:3245372,3251371_start:5713_stop:5733 +TAGCCTATAAGAGGTTAGGTG +>3L:3245372,3251371_start:5734_stop:5754 +TACCAAGGCGAACAATCAGCG +>3L:3245372,3251371_start:5755_stop:5775 +AAAACGGAATCGATTACAGTT +>3L:3245372,3251371_start:5776_stop:5796 +TTGGAGATCGTGAGAGGAGGA +>3L:3245372,3251371_start:5797_stop:5817 +GAAGAGGCGACTGCTTGATAA +>3L:3245372,3251371_start:5818_stop:5838 +GCCCGGACCCTCCAGCGATCT +>3L:3245372,3251371_start:5839_stop:5859 +CCAATCAATATTACTTTCCAC +>3L:3245372,3251371_start:5860_stop:5880 +CTACATATCTCCCCCTTTCAG +>3L:3245372,3251371_start:5881_stop:5901 +CTGGTTTAATTTTGGATTCCC +>3L:3245372,3251371_start:5902_stop:5922 +CCATCTGGCTGGCCTATTTTC +>3L:3245372,3251371_start:5923_stop:5943 +GCCTGGCCTGCGTTATTTATT +>3L:3245372,3251371_start:5944_stop:5964 +AGTTAATAAACCATTAATATA +>3L:3245372,3251371_start:5965_stop:5985 +TACTTGAATAAAAAGGCGTTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Apr 15 06:34:23 2015 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="biopython" version="1.65"> + <repository changeset_revision="f8d72690eeae" name="package_biopython_1_65" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>