# Download source files:

wget "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE173nnn/GSE173479/matrix/GSE173479_series_matrix.txt.gz"
#
# Information was extracted from the matrix file

zcat GSE173479_series_matrix.txt.gz | ./ghahhari22_extract_sample_info.pl  > samples

# ghahhari22_extract_sample_info.pl is a customized script for this series. 
# The code lines for extracting the feature field from the filename won't
# work for other matrix files.
#
## Generation of SGA files:

./ghahhari22_mk_sga.pl < samples | sh &

# Merged samples: 

# Replicates and experiments of the same type applied to different 
# passages of the same cell culture were merged. The driver input file 
# for merging the samples (merged_samples) was generated manually.
# Filenames of merged samples end with "merged.sga". Sample 
# descriptions of merged samples end with the tag "all". The preceding
# parts of the sample descriptions are sufficient to identify the
# members of the merged group of samples. Merging is done with a
# customized Perl script, which may not work for other samples. 

./ghahhari22_merge_samples.pl < merged_samples | sh &

# Generation of sample description file: 

cat samples merged_samples | ./ghahhari22_mk_txt.pl > ../ghahhari22.txt

# For quality control and analysis scripts, see ../analysis/scripts/README 
