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How to append two fasta files?

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# 8  
Old 06-13-2019
Scrutinizer:
Could you elaborate this part ?

Code:
FS=RS; RS=">";

I tried FS=RS=">"; but it did not work. What's the difference between the two: FS=RS; RS=">"; vs FS=RS=">";
# 9  
Old 06-13-2019
Hi yifangt,

The default value for RS is '\n'
So after FS=RS; RS=">" FS is '\n' and RS is '>'

If we use FS=RS=">", then they both become equal to '>'

S.
# 10  
Old 06-13-2019
Post #5 is interesting.
I found it can be enhanced, by a ^ anchor (match at the beginning only), and by inserting a ^ character that becomes an anchor for the following grep
Code:
tr $'\n>' $' \n' <file1|  grep -vf <(sed -n 's/^>/^/p' file2) | cat  <(tr $'\n>' $' \n' <file2) - |  tr  -s $' \n' $'\n>'

Post #7 did not work for me.? Did not further analyze it.
Here is an embedded multi-line awk code that works for me:
Code:
#!/bin/sh
awk '
{
  ishead=($1~/^>/)
}
FNR==NR {
  # file1: store everything in F[head]
  if (ishead) {
     head=$1
     sep=""
  } else {
     F[head]=(F[head] sep $1)
     sep=ORS
  }
  next
}
{
  # file2: print everything, delete corresponding F[head] from file1
  if (ishead) {
    delete F[$1]
  }
  print
}
END {
  # print the remaining F[head] from file1
  for (head in F) {
    print head
    print F[head]
  }
}
' file1 file2

I chose $1 not $0 because I found some trailing spaces in the given examples; spaces are stripped if $1 is used.
# 11  
Old 06-13-2019
Post #7 probably did not work for you because there are excess trailing spaces that need to be removed in the file samples, but that are not going to be present in the actual FASTA files, see the note underneath...

--
Here they are without the spaces:
File1:
Code:
>Contig_1:90600-91187
GACCGTCATCAATTCCTGTTCCTTGCCCTTGACGACCTCATCCACGTCCTTGATGGCCTT
>Contig_24:26615-28387
TTCGCCGCGCTCCAAACGGGCGATCTCCTCGGCGCGGGCCGCCAGGATCAGCGCCG
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG               
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGA

File2:
Code:
>Contig_1:90600-91187
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGGAATTGATGACGGTC
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGG
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGA
>Contig_24:26615-28387
GCTGCGGCGCTGATCCTGGCGGCCCGCGCCGAGGAGATCGCCCGTTTGGAGCGCGGCGAA

Of course another thing is the order that is mixed up when because it is undefined in the array structure in awk. That could easily be fixed of course if need be.
Last edited by Scrutinizer; 06-13-2019 at 06:12 PM..
This User Gave Thanks to Scrutinizer For This Post:
MadeInGermany
# 12  
Old 06-13-2019
Ah now I see - and you do not have the $1 workaround because you set a different RS...
After trimming the input files it worked.
This User Gave Thanks to MadeInGermany For This Post:
Scrutinizer
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