parse fasta file to tabular file Post: 302584663

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How to change sequence name in along fasta file?

Hi I have an alignment file (.fasta) with ~80 sequences. They look like this- >JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0 GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT...

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Change sequence names in fasta file

I have fasta files with multiple sequences in each. I need to change the sequence name headers from: >accD:_59176-60699 ATGGAAAAGTGGAGGATTTATTCGTTTCAGAAGGAGTTCGAACGCA >atpA_(reverse_strand):_showing_revcomp_of_10525-12048 ATGGTAACCATTCAAGCCGACGAAATTAGTAATCTTATCCGGGAAC...

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Hi, I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help . input > fefrwefrwef X900 AGAGGGAATTGG AGGGGCCTGGAG GGTTCTCTTC > fefrwefrwef X932 AGAGGGAATTGG AGGAGGTGGAG GGTTCTCTTC > fefrwefrwef X937...

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Extract sequences from a FASTA file based on another file

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How do we append the file name to fasta file headers in multiple fasta-files in Linux?

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Convert text file to HTML tabular format.

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Hi How can I extract sequences from a fasta file with respect a certain criteria? The beginning of my file (containing in total more than 1000 sequences) looks like this: >H8V34IS02I59VP SDACNDLTIALLQIAREVRVCNPTFSFRWHPQVKDEVMRECFDCIRQGLG YPSMRNDPILIANCMNWHGHPLEEARQWVHQACMSPCPSTKHGFQPFRMA...

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I have the following script: awk 'FNR==NR{s+=$3;next;} { print $1 , $2, 100*$3/s }' and the following file: >P39PT-1224 Freq 900 cccctacgacggcattggtaatggctcagctgctccggatcccgcaagccatcttggatatgagggttcgtcggcctcttcagccaagg-cccccagcagaacatccagctgatcg >P39PT-784 Freq 2...

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Hi, I have a fasta file with multiple sequences. How can i get only unique sequences from the file. For example my_file.fasta >seq1 TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC >seq2...

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viewperl

VIEWPERL(1)							   User Commands						       VIEWPERL(1)

NAME

       viewperl - quickly view syntax highlighted Perl code

SYNOPSIS

       viewperl [OPTION]... FILE...

DESCRIPTION

       View a Perl source code file, syntax highlighted.

       -c, --code=CODE
	      view CODE, syntax highlighted

       -l, --lines
	      display line numbers

       -L, --no-lines
	      supress display of line numbers (default)

       -m, --module=FILE
	      consider FILE the name of a module, not a file name

       -n, --name
	      display the name of each file (default)

       -N, --no-name
	      supress display of file names (implied by --no-reset)

       -p, --pod
	      display inline POD documentation (default)

       -P, --no-pod
	      hide POD documentation (line numbers still increment)

       -r, --reset
	      reset formatting and line numbers each file (default)

       -R, --no-reset
	      supress resetting of formatting and line numbers

       -s, --shift=WIDTH
	      set tab width (default is 4)

       -t, --tabs
	      translate tabs into spaces (default)

       -T, --no-tabs
	      supress translating of tabs into spaces

       --help display this help and exit

       Note that module names should be given as they would appear after a Perl `use' or `require' statement.  `Getopt::Long', for example.

       Each string given using -c is considered a different file, so line number and formatting resets will apply.

       View a Perl source code file, syntax highlighted.

       -c, --code=CODE
	      view CODE, syntax highlighted

       -l, --lines
	      display line numbers

       -L, --no-lines
	      supress display of line numbers (default)

       -m, --module=FILE
	      consider FILE the name of a module, not a file name

       -n, --name
	      display the name of each file (default)

       -N, --no-name
	      supress display of file names (implied by --no-reset)

       -p, --pod
	      display inline POD documentation (default)

       -P, --no-pod
	      hide POD documentation (line numbers still increment)

       -r, --reset
	      reset formatting and line numbers each file (default)

       -R, --no-reset
	      supress resetting of formatting and line numbers

       -s, --shift=WIDTH
	      set tab width (default is 4)

       -t, --tabs
	      translate tabs into spaces (default)

       -T, --no-tabs
	      supress translating of tabs into spaces

       --help display this help and exit

       Note that module names should be given as they would appear after a Perl `use' or `require' statement.  `Getopt::Long', for example.

       Each string given using -c is considered a different file, so line number and formatting resets will apply.

viewperl							    August 2007 						       VIEWPERL(1)