From 0ad7712a6bdc7aedfb5c536915be318a301c049a Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 4 Aug 2022 14:06:29 +0200
Subject: [PATCH] throw error when trying to write empty sequence in FASTA file
---
modules/io/src/seq/fasta_io_handler.cc | 12 +++++++++++-
1 file changed, 11 insertions(+), 1 deletion(-)
diff --git a/modules/io/src/seq/fasta_io_handler.cc b/modules/io/src/seq/fasta_io_handler.cc
index 48e7d474d..61bb43ba0 100644
--- a/modules/io/src/seq/fasta_io_handler.cc
+++ b/modules/io/src/seq/fasta_io_handler.cc
@@ -46,6 +46,12 @@ void FastaIOHandler::Import(seq::SequenceList& aln,
void FastaIOHandler::Export(const seq::ConstSequenceList& msa,
const boost::filesystem::path& loc) const {
+ // deliberately check for valid sequences BEFORE file is created on disk
+ for (int i=0; i<msa.GetCount(); ++i) {
+ if(msa[i].GetString().empty()) {
+ throw IOException("Cannot write FASTA file: Sequence is empty.");
+ }
+ }
boost::filesystem::ofstream outfile(loc);
this->Export(msa, outfile);
}
@@ -111,7 +117,8 @@ void FastaIOHandler::Import(seq::SequenceList& aln,
aln.AddSequence(seq);
seq_count+=1;
} catch (seq::InvalidSequence& e) {
- throw seq::InvalidSequence("Failed for sequence with name " + name + ": " + e.what());
+ throw seq::InvalidSequence("Failed for sequence \"" + name + "\" (" +
+ seq_string.str() + "): " + e.what());
}
} else {
throw IOException("Bad FASTA file: Sequence is empty.");
@@ -127,6 +134,9 @@ void FastaIOHandler::Export(const seq::ConstSequenceList& seqs,
std::ostream& ostream) const
{
for (int i=0; i<seqs.GetCount(); ++i) {
+ if(seqs[i].GetString().empty()) {
+ throw IOException("Cannot write FASTA file: Sequence is empty.");
+ }
ostream << ">" << seqs[i].GetName() << std::endl;
ostream << seqs[i].GetString() << std::endl;
}
--
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