![]() ![]() I'm not sure if this version is compatible with POSIX. Note: BioAwk is based on Brian Kernighan's awk which is documented in "The AWK Programming Language",īy Al Aho, Brian Kernighan, and Peter Weinberger It has all the bells-and-whistles from POSIX awk, but is augmented to easily process FASTA files: When you process fasta-files with awk, you can always concider to use bioawk. Concerning the adding of the contaminants, we are working on making SearchGUI download your favorite database automatically, add contaminants and decoys, and keep it up to date. $0=name if ($1 in a) print_sequence (name,seq) Gsub(seq_ere,"&" ORS, seq) print ">" name ORS seq A generic awk for processing fasta, looks like this: awk '/^>/ & seq Remark that, for the best way of processing, the sequence, should be stored as a continues string, and not contain any newlines or whitespaces due. Every time you read a full sequence, you can process it. The easiest way to process FASTA files with awk, is to build up a variable called name and a variable called seq. I had tried like this grep -f genelist.txt -A3 fastafile.txt > newfasta.txtīut different fasta sequences have different lengths,Īfter pattern match, i want to pick till next '>' symbol appears If the gene name and header line matches then, sequence has to be pulled out into new file GCGGCAAGGACCGTCACAGCAAGGTGAGGACGGTGAAGGGGCTCCGCGACCGGCGGGTGCGGCTGTCGGTGCCGACGGCGĪTCCAGCTCTACGACCTGCAGGACCGGCTGGGGCTCAGCCAGCCGAGCAAGGTGGTCGACT ![]() >LOC_Os05g43760.1 pacid=33158388 polypeptide=LOC_Os05g43760.1 locus=LOC_Os05g43760 ID=LOC_Os05g43760.1.MSUv7.0 annot-version=v7.0ĪTGACAAGCAATAACAGCACGAATGAGGAGCTCGGCGGCGGCGGCAGGAAGGCGGCCGACAAGCCGAGCGGCGGCGGCGGĬGCCGCCGCCGCCGTGGCGAGCTCGCGGCACTGGTCGGCGTCGACGGAGTCGCGGATCGTGCGCGTGTCGAGGGTGTTCG GCGCGGGTGTTCCAGCTGACGCGGGAGCTCGGGCACAAGACCGACGGCGA GACGTGCTCGACGTCGCAGACTGCCGGGGCGGGCGGCGGCGGCGTCGTGGGCGCGAATGGGTCGGCGGCGGCGGCGCCGCĬGAAGCGGACGTCGACGAAGGACCGGCACACGAAGGTGGACGGGCGGGGGCGGCGCATCCGGATGCCGGCGATCTGCGCC >LOC_Os06g12230.1 pacid=33145596 polypeptide=LOC_Os06g12230.1 locus=LOC_Os06g12230 ID=LOC_Os06g12230.1.MSUv7.0 annot-version=v7.0ĪTGGATGTCACCGGAGACGGCGGAGGAGGAGGGCAACGGCCCAATTTCCCCCTGCAGCTCCTCGGGAAGAAGGAGGAGCA GAAGGGAGGGGGCGGCGCATCCGGATGCCGGCGCTGTGCGCGGCGAGGGTGTTCCAGCTGACGCGGGAGCTGG >LOC_Os02g51280.1 pacid=33134358 polypeptide=LOC_Os02g51280.1 locus=LOC_Os02g51280 ID=LOC_Os02g51280.1.MSUv7.0 annot-version=v7.0ĪTGACCATGGACGTCGCCGGAGACGCCGGAGGTGGCCGCCGCCCAAACTTCCCCTTGCAGCTTCTTGAGAAGAAGGAGGAĬGGGCGGTGCCGGAGGGGAGATGCAGCTGCGGAAGGCGGCGCCGAAGCGGAGCTCCACCAAGGACCGGCACACCAAGGTG TACGACCTCCAGGACCGCCTCGGCTTCGACCAGCCGAGCAAGGCCATCGAGTGG GGAGATGGTGGAGGCGGTGTGGGGGCAGACGGGGAGTACGGCGTCGCGGATCTACAGGGTGAGGGCGACGGGGGGGAAGGĪCAGGCACAGCAAGGTGTACACGGCGAAGGGAATCCGCGACCGCCGCGTCCGCCTCTCCGTCGCCACCGCCATCCAGTTC The gene list file looks like this LOC_Os06g12230.1įasta sequence file looks like this >LOC_Os03g57190.1 pacid=33130570 polypeptide=LOC_Os03g57190.1 locus=LOC_Os03g57190 ID=LOC_Os03g57190.1.MSUv7.0 annot-version=v7.0ĪTGGAGGCGGCGGTGGGGGACGGGGAAGGCGGTGGCGGCGGCGGCGGGCGGGGGAAGCGTGGGCGGGGAGGAGGAGGAGG ![]()
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