別のfastaファイル内の完全なヘッダーの名前を知りたいです。

説明する内容を達成する1つの方法は次のとおりです。

1. ヘッダーを持つ2番目のファイルを使用してマッピングを作成する
2. 最初のファイルを読み、一致する行を地図上の一致に置き換えます。

たとえば、awk を使用します。

awk -F@ 'NR == FNR { if ($0 ~ /^>/) { a[$1] = $0 }; next } { if ($0 ~ /^>/ && $0 in a) $0 = a[$0]; print }' second_file_with_headers first_file

例:

$ cat second_file_with_headers
>TRINITY_DN100_c0_g1_i1 len=242 path=[0:0-241]@Guinardia_delicatula
AGCAATCCAAACTGCTGCAATCTGGGCTCGTGAAAACGATATGGTATTACACTTACACCGTGC
>TRINITY_DN100_c0_g1_i1 KR048205>TRINITY_DN105_c0_g1_i1 len=260 path=[0:0-259]AGCAATTCAAAGTGCTGCAATCTGGGCTCGTGAAAACGATATGTTATTACACTTACACCGTGCA
>TRINITY_DN103_c0_g1_i1 len=260 path=[0:0-259]@Luticola_sparsipunctata
AGCAATTCAAAGTGCTGCAATCTGGGCTCGTGAAAACGATATGATTTTACACTTACACCGTGCA

$ cat first_file
>TRINITY_DN100_c0_g1_i1 len=242 path=[0:0-241]
AGCAATTCAAACTGCTGCAATCTGGGCTCGTGAAAACGATATGGTATTACACTTACATCGTGCAAGACAAACAACAAGTGCGTTACGTCACGTTACGTTAATTCGTTCGTTCGTCTCTCTATTGCGTTGCGTTACGCTCTCGCCGCGGACCCAGCACCGCATACCCGCCCATACAAGTCATACAGTACACAACACAAAAACACAACCAACTATTTCCTTGGAAGAGAAAGCAAGCCCAAAAC
>TRINITY_DN105_c0_g1_i1 len=260 path=[0:0-259]
TGAAAATATTAATTCTCAACCTTTTATGCGTTGGAGAGAAAGATATTTATTTTCAATAGAGGGAGTTAATCGTGCAGCGGCAGCAAGTGGTGAAATTAAAGGACATTATTTAAATGTTACTGCAGGTACAATGGAAGACATGTACGAACGCGCCAAGATTGATGTGCCTGAGAACCACATGAATAACGAGGAGCAATACACACTTCACTACCAAGAGTACCTTGTGGGTAGCTCGGCTGGTGTGCCCAAGGATATGAAGG
>TRINITY_DN103_c0_g1_i1 len=260 path=[0:0-259]
GTTCTCTTCGGTGGCAGCCTTACGGCCGACCACCTGGTATTGTCGCATAATTCCCGCAGCAGTCATGATGTCTATTGTTTGTCGTGAAAAGAAATGAATTAAGAGAGTCATAGTTACTCCCGCCGTTTACCCGCGCTTGGTTGAATTCCTTCACTTTGACATTCAGAGCACTGGGCAGAAATCACATTGCGTCAACACCATCTCTGTTTCAACGAAATCAGCAGTATCTGTAGAAGTGTAGTTAAAACTAATATCTTTCC

$ awk -F@ 'NR == FNR { if ($0 ~ /^>/) { a[$1] = $0 }; next } { if ($0 ~ /^>/ && $0 in a) $0 = a[$0]; print }' second_file_with_headers first_file
>TRINITY_DN100_c0_g1_i1 len=242 path=[0:0-241]@Guinardia_delicatula
AGCAATTCAAACTGCTGCAATCTGGGCTCGTGAAAACGATATGGTATTACACTTACATCGTGCAAGACAAACAACAAGTGCGTTACGTCACGTTACGTTAATTCGTTCGTTCGTCTCTCTATTGCGTTGCGTTACGCTCTCGCCGCGGACCCAGCACCGCATACCCGCCCATACAAGTCATACAGTACACAACACAAAAACACAACCAACTATTTCCTTGGAAGAGAAAGCAAGCCCAAAAC
>TRINITY_DN105_c0_g1_i1 len=260 path=[0:0-259]
TGAAAATATTAATTCTCAACCTTTTATGCGTTGGAGAGAAAGATATTTATTTTCAATAGAGGGAGTTAATCGTGCAGCGGCAGCAAGTGGTGAAATTAAAGGACATTATTTAAATGTTACTGCAGGTACAATGGAAGACATGTACGAACGCGCCAAGATTGATGTGCCTGAGAACCACATGAATAACGAGGAGCAATACACACTTCACTACCAAGAGTACCTTGTGGGTAGCTCGGCTGGTGTGCCCAAGGATATGAAGG
>TRINITY_DN103_c0_g1_i1 len=260 path=[0:0-259]@Luticola_sparsipunctata
GTTCTCTTCGGTGGCAGCCTTACGGCCGACCACCTGGTATTGTCGCATAATTCCCGCAGCAGTCATGATGTCTATTGTTTGTCGTGAAAAGAAATGAATTAAGAGAGTCATAGTTACTCCCGCCGTTTACCCGCGCTTGGTTGAATTCCTTCACTTTGACATTCAGAGCACTGGGCAGAAATCACATTGCGTCAACACCATCTCTGTTTCAACGAAATCAGCAGTATCTGTAGAAGTGTAGTTAAAACTAATATCTTTCC

$

awkスクリプトは簡単に説明できます。

awk         # the awk program, can be gawk, mawk or any other implementation
-F@         # Sets FS="@" . This tells awk to split on the @ character.
NR == FNR { if ($0 ~ /^>/) { a[$1] = $0 }; next }
   # While handling the first argument (here, second_file_with_headers)
   # For lines starting with >, store the line into an array with the part before @ as the key
   # Discard all lines in this file with 'next'
{ if ($0 ~ /^>/ && $0 in a) $0 = a[$0]; print }
   # For all other lines, meaning that we are now working on the second argument (first_file)
   # For lines starting with >, change the line into the stored version from the array if it exists
   # then print the line
second_file_with_headers
   # Use the file with the headers as the first argument
first_file
   # Use the file which needs to be updated as the second argument