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Top Forums UNIX for Beginners Questions & Answers How to append two fasta files? Post 303035989 by vgersh99 on Tuesday 11th of June 2019 03:10:37 PM
Old 06-11-2019
Quote:
Originally Posted by yifangt
I put my answer back as I met the scenarios:
1) when file2.fasta contains more entries than in file1.fasta and vice versa. and
2) when the sequence part can have more than one row;
Code:
awk 'BEGIN{RS=">";FS="\n"} {A[$1]=$2} END{for (i in A) {if (i) print ">"i,FS,A[i]}}' file1.fasta file2.fasta

This only works for 2-line fasta sequence files (i.e. each entry has two lines, One starts with ">" as the header, the other is the DNA sequence. @vgersh99, could you please elaborate your code for scenario 2)? Thanks!
My previously posted attempt was for the provided sample files ONLY - 2 lines for each sequence: 1 header and 1 "data" lines.
Had the OP elaborated on the possible other sample data files, an alternate solution would have been provided.
This User Gave Thanks to vgersh99 For This Post:
 

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comm(1) 							   User Commands							   comm(1)

NAME
comm - select or reject lines common to two files SYNOPSIS
comm [-123] file1 file2 DESCRIPTION
The comm utility reads file1 and file2, which must be ordered in the current collating sequence, and produces three text columns as output: lines only in file1; lines only in file2; and lines in both files. If the input files were ordered according to the collating sequence of the current locale, the lines written will be in the collating sequence of the original lines. If not, the results are unspecified. OPTIONS
The following options are supported: -1 Suppresses the output column of lines unique to file1. -2 Suppresses the output column of lines unique to file2. -3 Suppresses the output column of lines duplicated in file1 and file2. OPERANDS
The following operands are supported: file1 A path name of the first file to be compared. If file1 is -, the standard input is used. file2 A path name of the second file to be compared. If file2 is -, the standard input is used. USAGE
See largefile(5) for the description of the behavior of comm when encountering files greater than or equal to 2 Gbyte ( 2**31 bytes). EXAMPLES
Example 1: Printing a list of utilities specified by files If file1, file2, and file3 each contain a sorted list of utilities, the command example% comm -23 file1 file2 | comm -23 - file3 prints a list of utilities in file1 not specified by either of the other files. The entry: example% comm -12 file1 file2 | comm -12 - file3 prints a list of utilities specified by all three files. And the entry: example% comm -12 file2 file3 | comm -23 -file1 prints a list of utilities specified by both file2 and file3, but not specified in file1. ENVIRONMENT VARIABLES
See environ(5) for descriptions of the following environment variables that affect the execution of comm: LANG, LC_ALL, LC_COLLATE, LC_CTYPE, LC_MESSAGES, and NLSPATH. EXIT STATUS
The following exit values are returned: 0 All input files were successfully output as specified. >0 An error occurred. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWesu | +-----------------------------+-----------------------------+ |CSI |enabled | +-----------------------------+-----------------------------+ |Interface Stability |Standard | +-----------------------------+-----------------------------+ SEE ALSO
cmp(1), diff(1), sort(1), uniq(1), attributes(5), environ(5), largefile(5), standards(5) SunOS 5.10 3 Mar 2004 comm(1)
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