Massive check of file open lines. Changed bareword filehandles
commit2d7429ae14b32fe8717cf19a695f451a1e85ef7c
authorFrancisco J. Ossandon <fco.j.ossandon@gmail.com>
Fri, 28 Feb 2014 16:22:49 +0000 (28 13:22 -0300)
committerFrancisco J. Ossandon <fco.j.ossandon@gmail.com>
Fri, 28 Feb 2014 16:22:49 +0000 (28 13:22 -0300)
treea1c69d83a096859e6a8d1ea6a5fd9b3edbd68c3f
parent8b47d9891571b102ad92e350a5c0e118a29c9253
Massive check of file open lines. Changed bareword filehandles
to lexical with three-argument opens calls, added die/throw
and reason of failure $! where missing, and made error messages
more uniform and consistent with Florent Angly messages for Root
(like quoting of filenames). Also deleted a few unused open
filehandles and some unnecessary parenthesis. Tests pass.
101 files changed:
Bio/Align/Graphics.pm
Bio/AlignIO.pm
Bio/Assembly/IO/bowtie.pm
Bio/Assembly/Tools/ContigSpectrum.pm
Bio/DB/BioFetch.pm
Bio/DB/Flat.pm
Bio/DB/Flat/BinarySearch.pm
Bio/DB/GFF.pm
Bio/DB/GFF/Adaptor/berkeleydb.pm
Bio/DB/HIV.pm
Bio/DB/Query/HIVQuery.pm
Bio/DB/Registry.pm
Bio/DB/SeqFeature/Store/DBI/Pg.pm
Bio/DB/SeqFeature/Store/DBI/SQLite.pm
Bio/DB/SeqFeature/Store/berkeleydb.pm
Bio/DB/SeqHound.pm
Bio/DB/TFBS/transfac_pro.pm
Bio/DB/Taxonomy/flatfile.pm
Bio/DB/Taxonomy/greengenes.pm
Bio/DB/Taxonomy/silva.pm
Bio/DB/WebDBSeqI.pm
Bio/Index/Abstract.pm
Bio/Index/Blast.pm
Bio/Index/BlastTable.pm
Bio/Index/EMBL.pm
Bio/Index/Fasta.pm
Bio/Index/Fastq.pm
Bio/Index/GenBank.pm
Bio/Index/Hmmer.pm
Bio/Index/Qual.pm
Bio/Index/Stockholm.pm
Bio/Index/SwissPfam.pm
Bio/Index/Swissprot.pm
Bio/LiveSeq/IO/Loader.pm
Bio/MapIO/fpc.pm
Bio/PhyloNetwork/GraphViz.pm
Bio/PullParserI.pm
Bio/SimpleAlign.pm
Bio/Tools/Alignment/Consed.pm
Bio/Tools/Lucy.pm
Bio/Tools/Run/RemoteBlast.pm
Bio/Tools/Run/WrapperBase/CommandExts.pm
Bio/Tools/ipcress.pm
Bio/Tree/Draw/Cladogram.pm
Bio/Tree/Tree.pm
Bio/Tree/TreeFunctionsI.pm
Build.PL
doc/Deobfuscator/bin/deob_index.pl
doc/Deobfuscator/cgi-bin/deob_interface.cgi
examples/contributed/rebase2list.pl
examples/db/rfetch.pl
examples/make_primers.pl
examples/subsequence.cgi
examples/tools/extract_genes.pl
maintenance/authors.pl
maintenance/check_URLs.pl
maintenance/cvs2cl_by_file.pl
maintenance/dependencies.pl
maintenance/deprecated.pl
maintenance/find_mod_deps.pl
maintenance/modules.pl
scripts/Bio-DB-GFF/bp_genbank2gff.pl
scripts/Bio-DB-GFF/bp_genbank2gff3.pl
scripts/Bio-DB-GFF/bp_process_gadfly.pl
scripts/das/bp_das_server.pl
scripts/popgen/bp_composite_LD.pl
scripts/searchio/bp_fastam9_to_table.pl
scripts/searchio/bp_hmmer_to_table.pl
scripts/searchio/bp_parse_hmmsearch.pl
scripts/searchio/bp_search2table.pl
scripts/seq/bp_split_seq.pl
scripts/seqstats/bp_chaos_plot.pl
scripts/seqstats/bp_oligo_count.pl
scripts/tree/bp_blast2tree.pl
scripts/utilities/bp_download_query_genbank.pl
scripts/utilities/bp_netinstall.pl
scripts/utilities/bp_revtrans-motif.pl
scripts/utilities/bp_search2tribe.pl
t/RemoteDB/HIV/HIVAnnotProcessor.t
t/RemoteDB/HIV/HIVQuery.t
t/SearchIO/blast.t
t/Seq/MetaSeq.t
t/SeqFeature/Collection.t
t/SeqIO/Handler.t
t/SeqIO/SeqIO.t
t/SeqIO/ace.t
t/SeqIO/embl.t
t/SeqIO/fasta.t
t/SeqIO/gcg.t
t/SeqIO/genbank.t
t/SeqIO/largefasta.t
t/SeqIO/mbsout.t
t/SeqIO/msout.t
t/SeqIO/raw.t
t/SeqIO/swiss.t
t/Tools/Genewise.t
t/Tools/Genomewise.t
t/Tools/Run/WrapperBase.t
t/Tree/TreeIO/newick.t
t/Tree/TreeIO/nhx.t
t/Variation/Variation_IO.t