FeatureCount2GCT

This is a script to convert the output from FeatureCount to GCT format expression tables

Why we need this

FeatureCount is quite useful and popular to analyse the gene expression level from RNA-seq datasets, and the GTEX eQTL pipeline requires expression tables in GCT format.

Dependencies:

Python3+
numpy

Manual

 $ python FC_2_GCT.py -h
usage: FC_2_GCT.py [-h] [-datadir [DATADIR]] [-out OUT] [-mergedata MERGEDATA]

Script to transform the output from featurecount to .gct format for eQTL
mapping

optional arguments:
  -h, --help            Show this help message and exit
  --datadir [DATADIR]   Script to transform a featureCounts output (cut -f1,7- removed) 
			to .gct format for eQTL mapping
  --out OUT             Output file prefix, by default it is "out", 
			i.e. Output will be out.gct and out.normalised.gct
  --mergedata MERGEDATA The input dir has one count input from featureCounts 
			containing all the samples. Set to 0 to turn it off

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Example

 $ ll featureCount/ 
total 4164520
-rw-r--r--  1 ningliu  staff    34M 17 Jan 11:44 ERR009096.counts.txt
-rw-r--r--  1 ningliu  staff   331B 17 Jan 11:45 ERR009096.counts.txt.summary
-rw-r--r--  1 ningliu  staff    34M 17 Jan 11:52 ERR009097.counts.txt
-rw-r--r--  1 ningliu  staff   331B 17 Jan 11:40 ERR009097.counts.txt.summary
-rw-r--r--  1 ningliu  staff    34M 17 Jan 11:44 ERR009099.counts.txt
-rw-r--r--  1 ningliu  staff   333B 17 Jan 11:55 ERR009099.counts.txt.summary
-rw-r--r--  1 ningliu  staff    34M 17 Jan 11:38 ERR009102.counts.txt
-rw-r--r--  1 ningliu  staff   334B 17 Jan 11:54 ERR009102.counts.txt.summary
-rw-r--r--  1 ningliu  staff    34M 17 Jan 11:42 ERR009103.counts.txt
-rw-r--r--  1 ningliu  staff   332B 17 Jan 11:48 ERR009103.counts.txt.summary
-rw-r--r--  1 ningliu  staff    34M 17 Jan 11:55 ERR009104.counts.txt
-rw-r--r--  1 ningliu  staff   334B 17 Jan 11:47 ERR009104.counts.txt.summary
-rw-r--r--  1 ningliu  staff    34M 17 Jan 11:53 ERR009105.counts.txt
....

python FC_2_GCT.py --datadir featureCount/ --mergedata 0

$ ll Mergedata 
total 29736
-rw-r--r--@ 1 ningliu  staff    15M  5 Apr 20:42 merge_all.counts.txt

python FC_2_GCT.py --datadir Mergedata/ --mergedata 1

the /data/ folder is expected to have featureCounts outputs end with ".counts.txt"

To do

Give meaningful info to the Description column.
Invoke help message when no parameter or file is set. e.g.

python ~/projects/Development/FeatureCount2GCT/FC_2_GCT.py
START!
Traceback (most recent call last):
  File "/Users/jbreen/projects/Development/FeatureCount2GCT/FC_2_GCT.py", line 107, in <module>
    with open(datafiles[0],"r") as fcfile:
IndexError: list index out of range