Strange error when trying to mess around with a text file created from STATA in Windows. When using awk to create the 9 column GFF file to use with SignalMap awk goes a little weird. The original data looks like this;

CHR1	101	.17989999
CHR1	151	.083400011
CHR1	301	-.125
CHR1	451	0
CHR1	501	.16670001
CHR1	601	.69999999
CHR1	651	.33329999
CHR1	751	.75
CHR1	801	0
CHR1	901	.25099999

And when you try to create a GFF file using awk, it goes weird like this;

[[email protected]]$ head Sample.txt |awk '{if($3>=0) print $1"\t.\tSAMPLE\t"$2"\t"$2+49"\t"$3"\t.\t.\t."}'
CHR1	.	.AMPLE	.01	150	.17989999
CHR1	.	.AMPLE	.51	200	.083400011
CHR1	.	.AMPLE	.51	500	0
CHR1	.	.AMPLE	.01	550	.16670001
CHR1	.	.AMPLE	.01	650	.69999999
CHR1	.	.AMPLE	.51	700	.33329999
CHR1	.	.AMPLE	.51	800	.75
CHR1	.	.AMPLE	.01	850	0
CHR1	.	.AMPLE	.01	950	.25099999

After 10 mins of banging my head on the table I realised that it was probably something to do with Windows/Unix formatting. So this solved it;

[[email protected]]$ dos2unix -n sample.txt sample_new.txt
[[email protected]]$ head sample_new.txt |awk '{if($3>=0) print $1"\t.\tSAMPLE\t"$2"\t"$2+49"\t"$3"\t.\t."}'
CHR1	.	SAMPLE 101	150	.17989999	.	.
CHR1	.	SAMPLE 151	200	.083400011	.	.
CHR1	.	SAMPLE 451	500	0	.	.
CHR1	.	SAMPLE 501	550	.16670001	.	.
CHR1	.	SAMPLE 601	650	.69999999	.	.
CHR1	.	SAMPLE 651	700	.33329999	.	.
CHR1	.	SAMPLE 751	800	.75	.	.
CHR1	.	SAMPLE 801	850	0	.	.
CHR1	.	SAMPLE 901	950	.25099999	.	.