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vastgroup / vast-tools

A toolset for profiling alternative splicing events in RNA-Seq data.
MIT License
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Template files in VASTDB cannot be uncompressed #50

Closed nuno-agostinho closed 8 years ago

nuno-agostinho commented 8 years ago

When trying to run VAST-TOOLS combine with uncompressed template files inside VASTDB, the program gives a warning but ultimately ends by saying the table was saved. The table is actually an almost empty file without the desired content.

Here follows the output shown (preceding output lines are omitted):

[vast combine]: Combining results into a single table
Smartmatch is experimental at /genedata/Resources/Software/vast-tools/bin/Add_to_FULL.pl line 127.
gzip: /genedata/Resources/Software/vast-tools/VASTDB/Hsa/TEMPLATES/Hsa.FULL.Template.txt.gz: No such file or directory
Use of uninitialized value $h in scalar chomp at /genedata/Resources/Software/vast-tools/bin/Add_to_FULL.pl line 79.
Use of uninitialized value $h in split at /genedata/Resources/Software/vast-tools/bin/Add_to_FULL.pl line 80.
Use of uninitialized value $header[0] in join or string at /genedata/Resources/Software/vast-tools/bin/Add_to_FULL.pl line 116, <STDIN> line 1.
Use of uninitialized value $header[1] in join or string at /genedata/Resources/Software/vast-tools/bin/Add_to_FULL.pl line 116, <STDIN> line 1.
Use of uninitialized value $header[2] in join or string at /genedata/Resources/Software/vast-tools/bin/Add_to_FULL.pl line 116, <STDIN> line 1.
Use of uninitialized value $header[3] in join or string at /genedata/Resources/Software/vast-tools/bin/Add_to_FULL.pl line 116, <STDIN> line 1.
Use of uninitialized value $header[4] in join or string at /genedata/Resources/Software/vast-tools/bin/Add_to_FULL.pl line 116, <STDIN> line 1.
Use of uninitialized value $header[5] in join or string at /genedata/Resources/Software/vast-tools/bin/Add_to_FULL.pl line 116, <STDIN> line 1.
[vast combine]: Final table saved as: /genedata/NunoA/PSI/vast_out/INCLUSION_LEVELS_FULL-Hsa2.tab
[vast combine]: Completed Tue Nov 10 16:14:27 2015
kcha commented 8 years ago

Hi @nuno-agostinho,

VAST-TOOLS expects the file Hsa.FULL.Template.txt.gz and not its uncompressed form. Unless you are doing some custom modifications, there should not be any reason to modify the contents of VASTDB.