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Home: Perl Programming Help: Beginner: How to delete certain lines from a file in perl

perlchaser Novice Aug 31, 2012, 9:04 AM Post #1 of 2 (754 views) How to delete certain lines from a file in perl Can't Post I have a file like the following (I am showing the first several dozens of lines here): ---------------------------- >91ES8_RN Satellite Rattus gaattctgttcgttccaagcgggaaaagcttgtaggaagttgactttgaagataaacacacagctagtgttttgcaaagtgaattgctgttacttggcnaataagcttagttttaagtggttctagakggtaaaaagcatacttttctatatagacaaaacatgcgtttcccagtctgaatcncacattctttggc >ALSAT_RN SAT Rattus norvegicus agctttgcagttttatgagatcccatttgtcgattcttgatcttagagcataagccattggtgttttgttcaggaaattttttccagtgcccatgtgttccagatgcttccctagtttttcttctattagtttgagtgtgtctggtttgatgtggaggtccttgatccacttggacttaagct >B1_Rn SINE1/7SL Rattus agccgggcggtggtggcgcacgcctttaatcccagcactcgggaggcagaggcaggcggatctctgagttcgaggccagcctggtctacagagtgagttccaggacagccagggctacacagagaaaccctgtctcgaaaaaacaaaa >B2_Rat1 SINE2/tRNA Rattus ggggctggagagatggctcagcggttaagagcaccgactgctcttccagaggtcctgagttcaattcccagcaaccacatggtggctcacaaccatctgtaatgggatctgatgccctcttctggtgtgtctgaagacagctacagtgtactcatatataataaataaataaatctttaaaaaaaaaa >B2_Rat2 SINE2/tRNA Rattus ggggctggagagatggctcagtggttaagagcactgactgctcttccagaggtcctgagttcaaatcccagcaaccacatggtggctcacaaccatctgtaatgagatctgatgccctcttctggtgtgtctgaagacagctacagtgtacttatatataataaataaataaatctttaaaaaaaaaa >B2_Rat3 SINE2/tRNA Rattus ggggctggagagatggctcagcggttaagagcactgactgctcttccagaggtcctgagttcaattcccagcaaccacatggtggctcacaaccatctgtaatgggatccgatgccctcttctggtgtgtctgaagacagcgacagtgtactcatataaaataaataaataaatctttaaaaaaaaaa >B2_Rat4 SINE2/tRNA Rattus ggggctggagagatggctcagcggttaagagcactgactgctcttccagaggtcctgagttcaattcccagcaaccacatggtggctcacaaccatctgtaatgggatccgatgccctcttctggtgtgtctgaagacagctacagtgtactcacatacataaaataaataaatctttaaaaaaaaaa ---------------------------------------- The 'name' right after the '>' sign is sort of my IDs. I have an array which have some IDs in it: @names = ('B2_Rat4', 'B2_Rat1'); What I am trying to do is: I want check if the 'ID' in my file is among the IDs in the '@names' array. If yes, then I want to delete these IDs as well as all the information associated with the IDs from the file (the information after the 'ID', and the several lines of sequences below it). Which is the efficient way to do it? Thank you very much! Jackie

Laurent_R Enthusiast Aug 31, 2012, 10:40 AM Post #2 of 2 (751 views) Re: [perlchaser] How to delete certain lines from a file in perl [In reply to] Can't Post If the size of your data is not too large, you could use a grep to find out whether your name is in the array. If you have really a lot of names, you'll probably want to copy the array in a a hash (the names in the array being the keys of the hash) and then check for each name whether it is found in the hash.

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