to generate a control file

[Chia-Yi Cheng]

Dear developer,

I was able to install and run the test files successfully. NextI would like to use GRIT for assembly including dozens of libraries. Therefore I'd like to know if GRIT has a script to generate the control file. Thank you. 

[Nathan Boley]

Dear Chia-Yi,

> I was able to install and run the test files successfully. NextI would like
> to use GRIT for assembly including dozens of libraries. Therefore I'd like
> to know if GRIT has a script to generate the control file.

There is no script, but the format is (heopfully) relatively straight-forward:

Lines that start with a '#' are comments
Further lines have 7 category types, delimited by white space:
sample_type, rep_id, assay, paired, stranded, read_type, and filename

Files with the same sample type are merged for exon construction, and
files with the same sample type *and* rep_id are used for
quantification. If a * is provided for rep_id, then the file is used
for element construction but not for quantification.

paired and stranded indicate whether the reads are paired and
stranded, respectively

read type should either be set to forward, backward, or auto. If
forward, then if the first pair of a read maps to the genome without
being reverse complemented then the read is assumed to have come from
a positive stranded gene. Backward is the reverse. Auto attempts to
infer this parameter from a provided reference annotation.

Finally, filename is the location of the file.

Does that help?

I would be happy to write a quick script that generates this file, but
am not sure exactly what it would entail. Could you please explain
what such a script would do?

Best, Nathan

[Chia-Yi Cheng]

Dear Nathan,

Thanks for your response. The format was clear and I was more curious to know if manual input is the only way to generate a control file. So I did a test run and keep getting the same error RNASeq must be paired. 

The command was,

run_grit.py --control sam.control.txt --reference /usr/local/scratch/EUK/ccheng/Arabidopsis_thaliana.TAIR10.23.gtf --fasta $TAIR10_fasta/TAIR10_Chr.all.fasta.fa -t 16

my control file looks like,

# comment line

#sample_type rep_id assay paired stranded read_type filename

SAM rep1 rnaseq false false auto /usr/local/scratch/EUK/ccheng/unique_TopHat/SAM/SRR949956_TopHat.run/accepted_hits.bam

SAM rep2 rnaseq false false auto /usr/local/scratch/EUK/ccheng/unique_TopHat/SAM/SRR949965_TopHat.run/accepted_hits.bam

SAM rep3 rnaseq false false auto /usr/local/scratch/EUK/ccheng/unique_TopHat/SAM/SRR949988_TopHat.run/accepted_hits.bam

SAM rep4 rnaseq false false auto /usr/local/scratch/EUK/ccheng/unique_TopHat/SAM/SRR949989_TopHat.run/accepted_hits.bam

and got the following error,

Traceback (most recent call last):

  File "/usr/local/bin/run_grit.py", line 5, in <module>

    pkg_resources.run_script('GRIT==1.1.3', 'run_grit.py')

  File "/usr/local/packages/python/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 505, in run_script

    self.require(requires)[0].run_script(script_name, ns)

  File "/usr/local/packages/python/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 1245, in run_script

    execfile(script_filename, namespace, namespace)

  File "/local/packages/python-2.7.3/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_grit.py", line 515, in <module>

    main()

  File "/local/packages/python-2.7.3/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_grit.py", line 487, in main

    elements = discover_elements(sample_data, args)

  File "/local/packages/python-2.7.3/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_grit.py", line 442, in discover_elements

    sample_data.get_reads(sample_type)

  File "/local/packages/python-2.7.3/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_grit.py", line 247, in get_reads

    rnaseq_reads = self._load_rnaseq_reads(sample_type, rep_id)

  File "/local/packages/python-2.7.3/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_grit.py", line 188, in _load_rnaseq_reads

    assert data.paired == 'true', "RNASeq reads must be paired"

AssertionError: RNASeq reads must be paired

Thank you for your help.