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Top Forums UNIX for Beginners Questions & Answers How to append two fasta files? Post 303035986 by yifangt on Tuesday 11th of June 2019 02:32:15 PM
Old 06-11-2019
combine and upgrade by the second fasta file

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!
Code:
file1.fasta
>Contig_1:90600-91187
GACCGTCATCAATTCCTGTTCCTTGCCCTTGACGACCTCATCCACGTCCTTGATGGCCTT 
>Contig_24:26615-28387
TTCGCCGCGCTCCAAACGGGCGATCTCCTCGGCGCGGGCCGCCAGGATCAGCGCCG
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG               
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGA

file2.fasta:
>Contig_1:90600-91187 
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGGAATTGATGACGGTC
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGG
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGA
>Contig_24:26615-28387
GCTGCGGCGCTGATCCTGGCGGCCCGCGCCGAGGAGATCGCCCGTTTGGAGCGCGGCGAA

output:
>Contig_1:90600-91187 
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGGAATTGATGACGGTC
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGG
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGA
>Contig_24:26615-28387
GCTGCGGCGCTGATCCTGGCGGCCCGCGCCGAGGAGATCGCCCGTTTGGAGCGCGGCGAA
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG               
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGA

This User Gave Thanks to yifangt For This Post:
 

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JOIN(1) 						      General Commands Manual							   JOIN(1)

NAME
join - relational database operator SYNOPSIS
join [ options ] file1 file2 DESCRIPTION
Join forms, on the standard output, a join of the two relations specified by the lines of file1 and file2. If file1 is `-', the standard input is used. File1 and file2 must be sorted in increasing ASCII collating sequence on the fields on which they are to be joined, normally the first in each line. There is one line in the output for each pair of lines in file1 and file2 that have identical join fields. The output line normally con- sists of the common field, then the rest of the line from file1, then the rest of the line from file2. Fields are normally separated by blank, tab or newline. In this case, multiple separators count as one, and leading separators are dis- carded. These options are recognized: -an In addition to the normal output, produce a line for each unpairable line in file n, where n is 1 or 2. -e s Replace empty output fields by string s. -jn m Join on the mth field of file n. If n is missing, use the mth field in each file. -o list Each output line comprises the fields specified in list, each element of which has the form n.m, where n is a file number and m is a field number. -tc Use character c as a separator (tab character). Every appearance of c in a line is significant. SEE ALSO
sort(1), comm(1), awk(1) BUGS
With default field separation, the collating sequence is that of sort -b; with -t, the sequence is that of a plain sort. The conventions of join, sort, comm, uniq, look and awk(1) are wildly incongruous. 7th Edition April 29, 1985 JOIN(1)
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