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added gzip support for RNA-Seq reads #697

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merged 1 commit into from
Nov 8, 2023
Merged

added gzip support for RNA-Seq reads #697

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10 changes: 4 additions & 6 deletions scripts/braker.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -2845,7 +2845,7 @@ sub find_tsebra_cfg {
# * priority in descending order: BAM, paired (_1/_2), paired(_R1/_R2), unpaired
################################################################################
sub check_rnaseq_sets{
my $fastq_file_extensions = "fastq|fq|fasta|fa";
my $fastq_file_extensions = "fastq|fq|fasta|fa|fastq.gz|fq.gz|fasta.gz|fa.gz";
my @dir_content;
$logString
.= "\# "
Expand Down Expand Up @@ -2892,7 +2892,7 @@ sub check_rnaseq_sets{

# search for paired or unpaired RNA-Sets in FASTQ format
# check if there are multiple RNA-Seq sets
@candidate_files = grep(/$rna_set(_1|_R1|).($fastq_file_extensions)$/, @dir_content);
@candidate_files = grep(/$rna_set(_1|_R1|).($fastq_file_extensions)$/, @dir_content);
if ($#candidate_files > 1) {
$logString .= "\# " . (localtime)
. " WARNING: Found more than one RNA-Seq Library in FASTQ format for $rna_set."
Expand All @@ -2906,10 +2906,8 @@ sub check_rnaseq_sets{
@candidate_files = grep(/${rna_set}${e}.($fastq_file_extensions)$/, @dir_content);
if (not ($e eq "")) {
foreach my $file (@candidate_files) {

my $ext1 = $e =~ s/1/2/r;
my ($ext2) = $file =~ /(\.[^.]+)$/;
my @candidate_pairs = grep(/${rna_set}${ext1}${ext2}/, @current_files);
my @candidate_pairs = grep(/${rna_set}${ext1}.($fastq_file_extensions)$/, @current_files);
if (@candidate_pairs) {
@curr_rna_lib = ($file, $candidate_pairs[0]);
$logString .= "\# " . (localtime)
Expand Down Expand Up @@ -4414,7 +4412,7 @@ sub make_bam_file {
. (localtime)
. ": Mapping RNA-Seq reads to the genome...\n" if ($v > 2);
foreach (keys(%rnaseq_libs)) {
# $string = join ",", @{$rnaseq_libs{$_}};

print LOG "\# "
. (localtime)
. ": Mapping $_ ...\n" if ($v > 1);
Expand Down
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