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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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DIFF(1) 						      General Commands Manual							   DIFF(1)

NAME
diff - print differences between two files SYNOPSIS
diff [-c | -e | -C n] [-br]file1 file2 OPTIONS
-C n Produce output that contains n lines of context -b Ignore white space when comparing -c Produce output that contains three lines of context -e Produce an ed-script to convert file1 into file2 -r Apply diff recursively to files and directories of EXAMPLES
diff file1 file2 # Print differences between 2 files diff -C 0 file1 file2 # Same as above diff -C 3 file1 file2 # Output three lines of context with every diff -c file1 file2 # Same diff /etc /dev # Compares recursively the directories /etc and /dev diff passwd /etc # Compares ./passwd to /etc/passwd DESCRIPTION
the same name, when file1 and file2 are both directories" difference encountered" Diff compares two files and generates a list of lines telling how the two files differ. Lines may not be longer than 128 characters. If the two arguments on the command line are both directories, diff recursively steps through all subdirectories comparing files of the same name. If a file name is found only in one directory, a diagnostic message is written to stdout. A file that is of either block special, character special or FIFO special type, cannot be compared to any other file. On the other hand, if there is one directory and one file given on the command line, diff tries to compare the file with the same name as file in the directory directory. SEE ALSO
cdiff(1), cmp(1), comm(1), patch(1). DIFF(1)
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