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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

Syntax
       mv [-i] [-f] [-] file1 file2

       mv [-i] [-f] [-] file... directory

Description
       The command 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, prints the mode and reads the
       standard input to obtain a line.  If the line begins with y, the move takes place.  If it does not, exits.  For further information, see

       In the second form, one or more files (plain files or directories) are moved to the directory with their original file-names.

       The command refuses to move a file onto itself.

Options
       -		   Interprets all following arguments as file names to allow file names starting with a minus.

       -f		   Force. This option overrides any mode restrictions or the -i switch.

       -i		   Interactive mode.  If a move is to supersede an existing file, the system prompts youw with the name of the	file  fol-
			   lowed  by  a question mark.	If you type a string that begins with y, the move occurs.  If you type any other response,
			   the move does not occur.

Restrictions
       If file1 and file2 lie on different file systems, 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.

See Also
       cp(1), ln(1)

																	     mv(1)
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