Steffen Möller pushed to branch master at Debian Med / bioperl
Commits: 3ac0f271 by Steffen Moeller at 2020-10-28T20:41:40+01:00 Introduced patch to parse old and new FT lines The specification of isoforms is not yet supported. - - - - - 2 changed files: - + debian/patches/FTlineParsingHickups.patch - + debian/patches/series Changes: ===================================== debian/patches/FTlineParsingHickups.patch ===================================== @@ -0,0 +1,38 @@ +Author: Steffen Moeller <[email protected]> +Title: Fix parsing of new UniProt FT lines +URL: https://github.com/bioperl/bioperl-live/pull/348 +Index: bioperl/lib/Bio/SeqIO/swiss.pm +=================================================================== +--- bioperl.orig/lib/Bio/SeqIO/swiss.pm ++++ bioperl/lib/Bio/SeqIO/swiss.pm +@@ -1289,7 +1289,7 @@ sub _read_FTHelper_swissprot { + $desc, # The descriptive text + $ftid, # feature Id is like a qualifier but there can be only one of them + ); +- if ( m/^FT\s{3}(\w+)\s+([\d\?\<]+)\s+([\d\?\>]+)\s*(.*)$/ox) { ++ if ( m/^FT\s{3}(\w+)\s+([\d\?\<]+)[\s.]+([\d\?\>]+)\s*(.*)$/ox) { + $key = $1; + my $loc1 = $2; + my $loc2 = $3; +@@ -1300,9 +1300,20 @@ sub _read_FTHelper_swissprot { + } else { + $desc = ""; + } ++ } elsif ( m/^FT\s{3}(\w+)\s+([\d\?\<]+)\s+(.*)$/ox) { ++ $key = $1; ++ my $loc1 = $2; ++ my $loc2 = $2; ++ $loc = "$loc1"; ++ if ($3 && (length($3) > 0)) { ++ $desc = $3; ++ chomp($desc); ++ } else { ++ $desc = ""; ++ } + } + +- while ( defined($_ = $self->_readline) && /^FT\s{20,}(\S.*)$/ ) { ++ while ( defined($_ = $self->_readline) && /^FT\s{4,}(\S.*)$/ ) { + my $continuation_line = $1; + if ( $continuation_line =~ /.FTId=(.*)\./ ) { + $ftid=$1; ===================================== debian/patches/series ===================================== @@ -0,0 +1 @@ +FTlineParsingHickups.patch View it on GitLab: https://salsa.debian.org/med-team/bioperl/-/commit/3ac0f27124dfc37fd2bd4b1c0165a2bf64dd1ede -- View it on GitLab: https://salsa.debian.org/med-team/bioperl/-/commit/3ac0f27124dfc37fd2bd4b1c0165a2bf64dd1ede You're receiving this email because of your account on salsa.debian.org.
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