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--- handy_custom_functions [2021/06/10 19:49] – 134.190.232.18
+++ handy_custom_functions [2023/07/25 12:08] (current) – 134.190.232.186
@@ Line 11: / Line 11: @@
 I will discuss here some more custom functions that I found are very useful in my daily workflow. To add these functions to your system, simply add them to your ''.bashrc''
-===Selecting or removing sequences from a FASTA file===
-<code>
-# fish out a sequence from a fasta file
-function grabseq {
-    fasta=$3
-    to_grab=$2
-    case "$1" in
-        -s) seqtk subseq $fasta <(grep    "$to_grab" $fasta | sed -e 's/>//' -e 's/ .*//');;
-        -l) seqtk subseq $fasta <(grep -f "$to_grab" $fasta | sed -e 's/>//' -e 's/ .*//');;
-        *) echo -e "grabseq -s <seqname> <fasta> to grab a single sequence\ngrab_seq -l <seqlist> <fasta> to grab a list of sequences"
-    esac
-}
-</code>
-This is essentially a wrapper for the [[https://github.com/lh3/seqtk|seqtk]] tool.
-<code>
-# select any sequence that has <pattern> in the header
-# useful if you want to find a single sequence
-$ grabseq -s <pattern> <FASTA>
-# select a particular set of sequences that have <pattern> in their header and are in the <pattern_list> file
-# useful if you want to multiple sequences
-$ grabseq -l <pattern_list> <FASTA>
-</code>
-The next function does the opposite of grabseq. It will remove particular sequences from a FASTA file.
-<code>
-# remove a particular entry from a fasta file
-function rmseq {
-    fasta=$3
-    to_rmv=$2
-    case "$1" in
-        -s) seqtk subseq $fasta <( grep ">" $fasta | grep -E -v "$to_rmv" | sed "s/>//" );;
-        -l) seqtk subseq $fasta <( grep ">" $fasta | grep -v -f "$to_rmv" | sed "s/>//" );;
-        *) echo -e "rmseq -s <seqname> <fasta> to remove a single sequence\nremove_seq -l <seqlist> <fasta> to remove a list of sequences"
-    esac
-}
-</code>
-<code>
-# remove a particular sequence that has <pattern> in the header
-$ rmseq -s <pattern> <FASTA>
-# remove a particular set of sequences that have <pattern> in the header and are in the <pattern_list> file
-$ rmseq -l <pattern_list> <FASTA>
-</code>
-NOTE: Dayana pointed out to me another tool similar to seqtk called [[https://github.com/shenwei356/seqkit|SeqKit]] which has a lot more functionality, essentially making the above custom functions obsolete.
-Selecting sequences:
-<code>
-# select a sequence with the exact <SeqID> as fasta header ID
-$ seqkit grep -p <SeqID> <FASTA>
-# select a sequence of which the fasta header ID matches a <regex_pattern>
-$ seqkit grep -rp <regex_pattern> <FASTA>
-# select a set of sequences of which the exact IDs are listed in <SeqID.exact.list>
-$ seqkit grep -f <SeqID.exact.list> <FASTA>
-# select a set of sequences of which the IDs match regex patterns listed in <SeqID.regex.list>
-$ seqkit grep -rf <SeqID.regex.list> <FASTA>
-</code>
-Removing sequences
-<code>
-# remove a sequence with the exact <SeqID> as fasta header ID
-$ seqkit grep -vp <SeqID> <FASTA>
-# remove a sequence of which the fasta header ID matches a <regex_pattern>
-$ seqkit grep -vrp <regex_pattern> <FASTA>
-# remove a set of sequences of which the exact IDs are listed in <SeqID.exact.list>
-$ seqkit grep -vf <SeqID.exact.list> <FASTA>
-# remove a set of sequences of which the IDs match regex patterns listed in <SeqID.regex.list>
-$ seqkit grep -vrf <SeqID.regex.list> <FASTA>
-</code>
-A FASTA header consists of two parts, the header ID and the header DESCRIPTION. The ID is essentially anything between ''>'' and the first space, and the DESCRIPTION is anything after that.
 ===Reformatting FASTA files downloaded from NCBI===