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Full Discussion: Issue in Script
Top Forums Shell Programming and Scripting Issue in Script Post 302971821 by rramkrishnas on Tuesday 26th of April 2016 05:40:00 AM
Old 04-26-2016
Issue in Script

I developed a script to group by 1st column and sum few of the column which are required, but while executing sum of 2nd column which has decimals in place is not getting correct sum. below is the script
Code:
 awk -F, '{a[$1]+=$2;b[$1]+=$33;c[$1]+=$58;d[$1]+=$11;e[$1]+=$50;}END{for(i in a)printf i","("%f\n"),a[i]","b[i]","c[i]","d[i]","e[i];}'  input.csv > "output.txt"

Attached the input and output file for furhter reference.
 

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FASTX_QUALITY_STATS(1)						   User Commands					    FASTX_QUALITY_STATS(1)

NAME
fastx_quality_stats - FASTX Statistics DESCRIPTION
usage: fastx_quality_stats [-h] [-N] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.13.2 by A. Gordon (gordon@cshl.edu) [-h] = This helpful help screen. [-i INFILE] = FASTQ input file. default is STDIN. [-o OUTFILE] = TEXT output file. default is STDOUT. [-N] = New output format (with more information per nucleotide/cycle). The *OLD* output TEXT file will have the following fields (one row per column): column = column number (1 to 36 for a 36-cycles read solexa file) count = number of bases found in this column. min = Lowest quality score value found in this column. max = Highest quality score value found in this column. sum = Sum of quality score values for this column. mean = Mean quality score value for this column. Q1 = 1st quartile quality score. med = Median quality score. Q3 = 3rd quartile quality score. IQR = Inter-Quartile range (Q3-Q1). lW = 'Left-Whisker' value (for boxplotting). rW = 'Right-Whisker' value (for boxplotting). A_Count = Count of 'A' nucleotides found in this column. C_Count = Count of 'C' nucleotides found in this column. G_Count = Count of 'G' nucleotides found in this column. T_Count = Count of 'T' nucleotides found in this column. N_Count = Count of 'N' nucleo- tides found in this column. max-count = max. number of bases (in all cycles) The *NEW* output format: cycle (previously called 'column') = cycle number max-count For each nucleotide in the cycle (ALL/A/C/G/T/N): count = number of bases found in this column. min = Lowest quality score value found in this column. max = Highest quality score value found in this column. sum = Sum of quality score values for this column. mean = Mean quality score value for this column. Q1 = 1st quartile quality score. med = Median quality score. Q3 = 3rd quartile quality score. IQR = Inter-Quartile range (Q3-Q1). lW = 'Left-Whisker' value (for boxplotting). rW = 'Right-Whisker' value (for boxplotting). SEE ALSO
The quality of this automatically generated manpage might be insufficient. It is suggested to visit http://hannonlab.cshl.edu/fastx_toolkit/commandline.html to get a better layout as well as an overview about connected FASTX tools. fastx_quality_stats 0.0.13.2 May 2012 FASTX_QUALITY_STATS(1)
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