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#!/bin/sh
#
# CHECK-entries.sh
# Marco van Zwetselaar <zwets@kcri.ac.tz>
#
# Checks that each sequence in the fsa files has an entry in phenotypes.txt,
# and that every entry in phenotypes has a corresponding sequence in an fsa.
#
# Writes to stdout the lists of missing entries, as well as close matches
# based on allele ID or accession.
#
# Echo all identifiers from the phenotypes.txt file, one per line.
phenotype_ids() {
cut -f1 phenotypes.txt | tail -n +2 | sed -e 's/ *$//'
}
# Echo all sequence identifiers from the *.fsa, one per line.
sequence_ids() {
fgrep -h '>' *.fsa | sed -e 's/>\([^ ]*\).*/\1/'
}
# Filter stdin for near matches of seqid $1. A near match is when either
# the allele ID (without accession) or the accession matches.
near_matches() {
# Horrid REGEX, but we need to escape special chars and split the SEQID
local REGEX="$(echo "$1" |
sed -e 's,\([][().+?|*]\),\\\1,g' \
-e 's,^\([^_]*_[^_]*\)\(_.*\),^\1|\2$,')"
grep -E "$REGEX" | tr '\n' ' '
}
printf "
===============================================================================
I. Entries in phenotypes.txt with trailing whitespace in their identifier (col 1).
(This whitespace breaks simple key based lookups.)
-------------------------------------------------------------------------------\n"
cut -f1 phenotypes.txt | tail -n +2 | fgrep ' '
printf "
===============================================================================
II. Entries in phenotypes.txt with no matching sequence in an *.fsa file.
Second column lists close matches (having identical alleleID or accession).
-------------------------------------------------------------------------------\n"
phenotype_ids | while read SEQID; do
sequence_ids | fgrep -xq "${SEQID}" ||
printf "$SEQID\t%s\n" "$(sequence_ids | near_matches "$SEQID")"
done
printf "
===============================================================================
III. Sequences in *.fsa that have no corresponding entry in phenotypes.txt.
Second column lists close matches (having identical alleleID or accession).
-------------------------------------------------------------------------------\n"
sequence_ids | while read SEQID; do
phenotype_ids | fgrep -xq "${SEQID}" ||
printf "$SEQID\t%s\n" "$(phenotype_ids | near_matches "$SEQID")"
done
# vim: sts=4:sw=4:si:et:ai
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