gravatar for amitpande74

3 hours ago by

Hi,
I have a fasta file formatted like this, product of paired end:

test_MAPQ.fasta->chr10:141146-141296
test_MAPQ.fasta:atgctcccattccaaatgagagtaattggctaaaacaaaggggctacaggtcccatacaagtccaaaacccaacagggcagtcattaaatcttTTCTAAttttaatttttattttatttgaagttctggggtacatgttcaggatgtata
test_MAPQ.fasta->chr10:142926-143076
--
test_MAPQ.fasta->chr10:146793-146943
test_MAPQ.fasta:gccAAATCATTACTTTTGAAGAAATAGTTAACAATGATTATTTCTTTTTGAATGACaataaattttattaataagttaaacatatttatatgtaatgtaaattttttGTATcgggtgcagtggttcatgcccgttatcctagcactttgg
test_MAPQ.fasta->chr10:146870-147020
test_MAPQ.fasta:aaacatatttatatgtaatgtaaattttttGTATcgggtgcagtggttcatgcccgttatcctagcactttgggaggccaaggtgttaatattgcttgagcaggggagtttgagaccagcctgggaaacatggtgaaacctcatatctac

I want an output where only both the pairs are included in the final results.

test_MAPQ.fasta->chr10:146793-146943
test_MAPQ.fasta:gccAAATCATTACTTTTGAAGAAATAGTTAACAATGATTATTTCTTTTTGAATGACaataaattttattaataagttaaacatatttatatgtaatgtaaattttttGTATcgggtgcagtggttcatgcccgttatcctagcactttgg
test_MAPQ.fasta->chr10:146870-147020
test_MAPQ.fasta:aaacatatttatatgtaatgtaaattttttGTATcgggtgcagtggttcatgcccgttatcctagcactttgggaggccaaggtgttaatattgcttgagcaggggagtttgagaccagcctgggaaacatggtgaaacctcatatctac

and the rest are ignored (like the upper pairs ending in dashes).
Is there a tool which can filter out the results ?
Kindly help.



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