Add basic script to check directory content against the manifests #10
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Add basic script to check directory content against the manifests #10sarahhunt wants to merge 1 commit into
sarahhunt wants to merge 1 commit into
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likhitha-surapaneni
requested changes
Sep 13, 2023
| my $ftp = Net::FTP->new("ftp.1000genomes.ebi.ac.uk", Debug => 0)|| die "Cannot connect to ftp.1000genomes.ebi.ac.uk: $@"; | ||
| $ftp->login("anonymous",'-anonymous@') || die "Cannot login ", $ftp->message; | ||
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| open my $dir_list, $ARGV[0] || die "Failed to open dir list $ARGV[0] : $!\n"; |
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| open my $dir_list, $ARGV[0] || die "Failed to open dir list $ARGV[0] : $!\n"; | |
| open my $dir_list, $ARGV[0] or die "Failed to open dir list $ARGV[0] : $!\n"; |
Interestingly, the code behaves differently for or and || when there is a file opening error. Tested with perl 5.26
| my $data_file_list = $ftp->dir(); | ||
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| ## write list of all & download manifest | ||
| open my $out, ">", "$dir\_data_file_list" ||die "Failed to open file to write list of data files for $dir :$!\n"; |
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| open my $out, ">", "$dir\_data_file_list" ||die "Failed to open file to write list of data files for $dir :$!\n"; | |
| open my $out, ">", "$dir\_data_file_list" or die "Failed to open file to write list of data files for $dir :$!\n"; |
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| ## check files in manifest available & get sizes | ||
| open my $size_log, ">$dir\_data_file_sizes" ||die "Failed to open file to write sizes of data files :$!\n"; |
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| open my $size_log, ">$dir\_data_file_sizes" ||die "Failed to open file to write sizes of data files :$!\n"; | |
| open my $size_log, ">$dir\_data_file_sizes" or die "Failed to open file to write sizes of data files :$!\n"; |
| foreach my $mani ( keys %get){ | ||
| print "starting on manifest $mani\n"; | ||
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| open my $filelist, $mani || die "Failed to read manifest $mani :$!\n"; |
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| open my $filelist, $mani || die "Failed to read manifest $mani :$!\n"; | |
| open my $filelist, $mani or die "Failed to read manifest $mani :$!\n"; |
| $ftp->cwd("$ftp_dir/$dir") || die "Cannot change project directory to $ftp_dir/$dir ", $ftp->message; | ||
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| ## get list of data files per dir | ||
| my $data_file_list = $ftp->dir(); |
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This is not giving a recursive list according to docs. Do we want to list the files recursively?
Sometimes the manifest file may not be in the root directory, we may miss the manifest file in this case unless we have a convention to have the manifest file in the root directory always.
Ex: 20220711_Strandseq
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