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Re: simple perl script to trim a FASTA file

by almut (Canon)
on Apr 08, 2010 at 22:10 UTC ( #833648=note: print w/ replies, xml ) Need Help??

in reply to simple perl script to trim a FASTA file

trim off x nucleotides from the beginning, and y nucleotides from the end
#!/usr/bin/perl while (<DATA>) { s/^(?!>)...(.*)..../$1/; # ^^^ ^^^^ # x=3 y=4 print; } __DATA__ >HWI-EAS158_40_3_1_46_535 GTGAATGCGTGATACAGGAATGTTCGTTGTGACCAT >HWI-EAS158_40_3_1_47_579 AAAGTGAATGCGTGATACAGGAATGTTCGTTGTGAC >HWI-EAS158_40_3_1_46_731 GTGTCATGCGTGATACAGGAATGTTCGTTGTGAAAA

For longer stretches you can also write .{N} (with N being the number of nucleotides to trim).

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