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Top Forums UNIX for Beginners Questions & Answers How to append two fasta files? Post 303036022 by RudiC on Wednesday 12th of June 2019 06:10:31 PM
Old 06-12-2019
May I paraphrase your request: You want file2's sequences to prevail and file1's sequences inserted only if there's no equivalent in file2. If so, try
Code:
tr $'\n>' $' \n' <file1|  grep -vf <(sed -n 's/>//p' file2) | cat  <(tr $'\n>' $' \n' <file2) - |  tr  -s $' \n' $'\n>'
>Contig_1:90600-91187
GACCGTCATCAATTCCTGTTCCTTGCCCTTGACGACCTCATCCACGTCCTTGATGGCCTT
>Contig_24:26615-28387
TTCGCCGCGCTCCAAACGGGCGATCTCCTCGGCGCGGGCCGCCAGGATCAGCGCCG
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG
>

with any length fasta sequences. The traiing ">" can be taken care of piping through | sed '$d' if need be. Please be aware that your desired output's "Contig_98" line is missing an "AG" at the end.

Last edited by RudiC; 06-13-2019 at 05:00 AM..
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MV(1)							      General Commands Manual							     MV(1)

NAME
mv - move or rename files SYNOPSIS
mv [ -i ] [ -f ] [ - ] file1 file2 mv [ -i ] [ -f ] [ - ] file ... directory DESCRIPTION
Mv moves (changes the name of) file1 to file2. If file2 already exists, it is removed before file1 is moved. If file2 has a mode which forbids writing, mv prints the mode (see chmod(2)) and reads the standard input to obtain a line; if the line begins with y, the move takes place; if not, mv exits. In the second form, one or more files (plain files or directories) are moved to the directory with their original file-names. Mv refuses to move a file onto itself. Options: -i stands for interactive mode. Whenever a move is to supercede an existing file, the user is prompted by the name of the file followed by a question mark. If he answers with a line starting with 'y', the move continues. Any other reply prevents the move from occur- ring. -f stands for force. This option overrides any mode restrictions or the -i switch. - means interpret all the following arguments to mv as file names. This allows file names starting with minus. SEE ALSO
cp(1), ln(1) BUGS
If file1 and file2 lie on different file systems, mv must copy the file and delete the original. In this case the owner name becomes that of the copying process and any linking relationship with other files is lost. 4th Berkeley Distribution April 29, 1985 MV(1)
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