seqkit grep without converting to unique patterns

[alvanuffelen]

Prerequisites

• make sure you're are using the latest version by seqkit version
• read the usage

Describe your issue

I have a FASTQ file from which I would like to subsample very specific sequences by ID. Additionally, some sequences should be subsampled multiple times. However, using seqkit grep with --pattern-file, it extracts each pattern only once.

seqkit grep -f id_list.txt mock.fq
[INFO] 3 patterns loaded from file

The file contains 4 patterns (2 unique and 1 duplicate). Would it be possible to add a parameter such that the patterns are not converted to unique patterns?

In contrast, seqtk does not only extract unique IDs:
seqtk subseq mock.fq id_list.txt
All 4 patterns are used, so the output contains 4 sequences.

mock.fq

@seq1
GATCGATCGA
+
IIIIIIIIII
@seq2
AGCTAGCTAG
+
IIIIIIIIII
@seq3
TACGTACGTA
+
IIIIIIIIII
@seq4
CGATCGATCG
+
IIIIIIIIII
@seq5
ATCGATCGAT
+
IIIIIIIIII
@seq6
GCTAGCTAGC
+
IIIIIIIIII
@seq7
CATGCATGCA
+
IIIIIIIIII
@seq8
TGCATGCATG
+
IIIIIIIIII
@seq9
AGCTAGCTAG
+
IIIIIIIIII
@seq10
ATCGATCGAT
+
IIIIIIIIII

id_list.txt

seq1
seq1
seq2
seq3

[shenwei356]

Added

  -D, --allow-duplicated-patterns   output records multiple times when duplicated patterns are given

• seqkit_darwin_amd64.tar.gz
• seqkit_darwin_arm64.tar.gz
• seqkit_linux_amd64.tar.gz