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nsalomonis / altanalyze

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.
http://www.altanalyze.org
Apache License 2.0
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Error in altanalyze calling getopt.py #37

Closed tmari closed 4 years ago

tmari commented 5 years ago

Hi!

I want to use AltAnalyze for my RNA-seq data (specifically to determine transcripts TPMs and splice junctions). I ran altanalyze as follows:

altanalyze --platform "RNASeq" --species Hs -fastq_dir /fast/work/users/tmari_m/nbp_project/alt_test/ --groupdir /fast/work/users/tmari_m/nbp_project/alt_test/groups.txt --compdir /fast/work/users/tmari_m/nbp_project/alt_test/comps.txt --output /fast/work/users/tmari_m/nbp_project/alt_test/output --expname test

but the software immediately stops giving this error message:

`Arguments input: ['AltAnalyze.py', '--platform', 'RNASeq', '--species', 'Hs', '-fastq_dir', '/fast/work/users/tmari_m/nbp_project/alt_test/', '--groupdir', '/fast/work/users/tmari_m/nbp_project/alt_test/groups.txt', '--compdir', '/fast/work/users/tmari_m/nbp_project/alt_test/comps.txt', '--output', '/fast/work/users/tmari_m/nbp_project/alt_test/output', '--expname', 'test']

Traceback (most recent call last): File "AltAnalyze.py", line 6347, in commandLineRun 'downsample=','query=','referenceFull=']) File "/fast/users/tmari_m/work/miniconda/lib/python2.7/getopt.py", line 90, in getopt opts, args = do_shorts(opts, args[0][1:], shortopts, args[1:]) File "/fast/users/tmari_m/work/miniconda/lib/python2.7/getopt.py", line 190, in do_shorts if short_has_arg(opt, shortopts): File "/fast/users/tmari_m/work/miniconda/lib/python2.7/getopt.py", line 206, in short_has_arg raise GetoptError('option -%s not recognized' % opt, opt) GetoptError: option -f not recognized

There is an error in the supplied command-line arguments (each flag requires an argument) ` Do you have any idea what could be the issue? Thank you!

nsalomonis commented 5 years ago

Greetings, The command-line options for AltAnalyze require two hyphens and one is missing in the --fastq_dir. Additionally, the option --runKallisto yes should be included, which should allow for the full analysis. For additional details on commands to use, see: https://github.com/nsalomonis/altanalyze/wiki/CommandLineMode