Hi @dariober

I was trying to findout the presence of G4's in the promoter sequences of my multifasta file

1. The expression you mentioned in the Readme.md file i.e. '([gG]{3,}\w{1,7}){3,}[gG]{3,}' for G3L1-7 identification, I think, will give me non-overlaping G4's if any. Will it report overlapping G4's too if present. I learned about searching G4's in this way from this paper.

xacct.py -v
xacct.py 0.3.0

Sort by MaxRSS gives:

xacct.py -s MaxRSS
Traceback (most recent call last):
  File "/home/db291g/bin/xacct.py", line 341, in <module>
    sacct_mrg= sorted(sacct_mrg, key=lambda k: k[s], reverse= rev)
TypeError: '<' not supported between instances of 'str' and 'int'

Probably due to a mix of numbers and strings in the sort field:

xacct.py
64377  WW00295.chr14.pindelChrom  node25    9027    48000   8          COMPLETED  Mon 25 15:44:36  02:29:10  
64413  WW00300.chr4.pindelChrom   node25    .       48000   8          RUNNING    Mon 25 15:44:36  00:07:03  
64561  WW00284.chr9.pindelChrom   .         .       48000   0          PENDING    Mon 25 15:44:39  00:00:00  
64339  WW00275.chr4.pindelChrom   node07    10753   48000   8          COMPLETED  Mon 25 15:50:45  05:52:27  
64414  WW00300.chr20.pindelChrom  node07    .       48000   8          RUNNING    Mon 25 15:50:45  00:00:54  
64562  WW00307.chr5.pindelChrom   .         .       48000   0          PENDING    Mon 25 15:51:11  00:00:00  

Hi,

Thank you for providing your useful tools.

There is a minor issue with the documentation (output from -h) in the script catInterleaveFastq.sh:

The usage instructions says

USAGE
catInterleaveFastq.sh -1 R1.L001.fq.gz R1.L002.fq.gz ... \\
                      -2 R2.L001.fq.gz R2.L002.fq.gz ...
First and second arguments are comma separated lists of first-in-pair and 
second-in-pair fastq file(s), respectively.

Clearly, the first and second arguments are not comma separated lists, but white-space separated lists -- just as correctly given in the example.

Cheers
Johan

Hi, Perhaps it's not an issue but my lack of understanding of the syntax, but I am not able to perform fuzzy regex seatch with your script. The syntax I am using is
-r "(ATGC){e<=1}"

It is not reporting any hits, whereas both exact and fuzzy matches exist in my input. Exact match without {e<=1} works just fine. Thank you.

Important TODO: tableCat.py needs to check that gzip exits clean!

I'm confused about the ref.fa file? is this publicly available or something I should have with my data?