#UNIX Assignment

##Data Inspection ###Attributes of fang_et_al_genotypes By inspecting this file I learned that: 1.line:2783 word: 2744038 byte:11051939 filename:fang_et_al_genotypes.txt 2.column of fang_et_al_genotypes.txt: 986

###Attributes of snp_position.txt By inspecting this file I learned that: 1.line:984 word:13198 byte:82763 filename:snp_position.txt 2.column of snp_position.txt: 15

##Data Processing
$ egrep "ZMMLR|ZMMIL|ZMMMR|Sample_ID" fang_et_al_genotypes.txt > maize_fang_et_al_genotypes.txt #grep ZMMLR or ZMMIL or ZMMMR $ egrep "ZMPBA|ZMPIL|ZMPJA|Sample_ID" fang_et_al_genotypes.txt > teosinte_fang_et_al_genotypes.txt #grep ZMPBA, ZMPIL, and ZMPJA $ awk -f transpose.awk teosinte_fang_et_al_genotypes.txt > teosinte_transposed_genotypes.txt $ awk -f transpose.awk maize_fang_et_al_genotypes.txt > maize_transposed_genotypes.txt $ mkdir Data-Processing-process ###Teosinte Data $ sed -i '1,3d' maize_transposed_genotypes.txt teosinte_transposed_genotypes.txt #delete Sample_ID, JG_OTU, and Group lines $ sed '1d' snp_position.txt > snp_position_nonhead.txt #delete the head of snp $ sort -k1,1V snp_position_nonhead.txt > snp_position_nonhead_sorted.txt #sort and save snp $ sort -k1,1V maize_transposed_genotypes.txt > maize_transposed_genotypes_sorted.txt #sort maize $ sort -k1,1V teosinte_transposed_genotypes.txt > teosinte_transposed_genotypes_sorted.txt #sort teosinte $ join -1 1 -2 1 -t $'\t' snp_position_nonhead_sorted.txt maize_transposed_genotypes_sorted.txt > maize_transposed_genotypes_joined.bed #join snp with maize $ join -1 1 -2 1 -t $'\t' snp_position_nonhead_sorted.txt teosinte_transposed_genotypes_sorted.txt > teosinte_transposed_genotypes_joined.bed #join snp with teosinte ##teosinte: $ sort -k3,3 teosinte_transposed_genotypes_joined.bed > teosinte_transposed_genotypes_joined_chr.bed #sort based on chrom colum $ grep -v "^#" teosinte_transposed_genotypes_joined_chr.bed | cut -f3 | uniq -c #count chromosome output:155 1 53 10 127 2 107 3 91 4 122 5 76 6 97 7 62 8 60 9 6 multiple 27 unknown $ sed -n '1,155p' teosinte_transposed_genotypes_joined_chr.bed > teosinte_transposed_genotypes_joined_chr1.bed #chrom1 $ sed -n '156,208p' teosinte_transposed_genotypes_joined_chr.bed > teosinte_transposed_genotypes_joined_chr10.bed $ sed -n '209,335p' teosinte_transposed_genotypes_joined_chr.bed > teosinte_transposed_genotypes_joined_chr2.bed $ sed -n '336,442p' teosinte_transposed_genotypes_joined_chr.bed > teosinte_transposed_genotypes_joined_chr3.bed $ sed -n '443,533p' teosinte_transposed_genotypes_joined_chr.bed > teosinte_transposed_genotypes_joined_chr4.bed $ sed -n '534,655p' teosinte_transposed_genotypes_joined_chr.bed > teosinte_transposed_genotypes_joined_chr5.bed $ sed -n '656,731p' teosinte_transposed_genotypes_joined_chr.bed > teosinte_transposed_genotypes_joined_chr6.bed $ sed -n '732,828p' teosinte_transposed_genotypes_joined_chr.bed > teosinte_transposed_genotypes_joined_chr7.bed $ sed -n '829,890p' teosinte_transposed_genotypes_joined_chr.bed > teosinte_transposed_genotypes_joined_chr8.bed $ sed -n '891,950p' teosinte_transposed_genotypes_joined_chr.bed > teosinte_transposed_genotypes_joined_chr9.bed $ sed -n '951,956p' teosinte_transposed_genotypes_joined_chr.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_transposed_genotypes_joined_mutiple.bed $ sed -n '957,983p' teosinte_transposed_genotypes_joined_chr.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_transposed_genotypes_joined_unknown.bed #teosinte: increasing position values and with missing data encoded by "-" $ sort -k4,4V teosinte_transposed_genotypes_joined_chr9.bed >/home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr9_ordered_increased.bed $ sort -k4,4V teosinte_transposed_genotypes_joined_chr8.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr8_ordered_increased.bed $ sort -k4,4V teosinte_transposed_genotypes_joined_chr7.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr7_ordered_increased.bed $ sort -k4,4V teosinte_transposed_genotypes_joined_chr6.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr6_ordered_increased.bed $ sort -k4,4V teosinte_transposed_genotypes_joined_chr5.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr5_ordered_increased.bed $ sort -k4,4V teosinte_transposed_genotypes_joined_chr4.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr4_ordered_increased.bed $ sort -k4,4V teosinte_transposed_genotypes_joined_chr3.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr3_ordered_increased.bed $ sort -k4,4V teosinte_transposed_genotypes_joined_chr2.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr2_ordered_increased.bed $ sort -k4,4V teosinte_transposed_genotypes_joined_chr1.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr1_ordered_increased.bed $ sort -k4,4V teosinte_transposed_genotypes_joined_chr10.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr10_ordered_increased.bed

#teosinte: decreasing position values and with missing data encoded by "-" $ sed 's/?/-/g' teosinte_transposed_genotypes_joined_chr8.bed | sort -k4,4nr > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr8_ordered_decreased.bed $ sed 's/?/-/g' teosinte_transposed_genotypes_joined_chr1.bed | sort -k4,4nr > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr1_ordered_decreased.bed $ sed 's/?/-/g' teosinte_transposed_genotypes_joined_chr2.bed | sort -k4,4nr > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr2_ordered_decreased.bed $ sed 's/?/-/g' teosinte_transposed_genotypes_joined_chr3.bed | sort -k4,4nr >/home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr3_ordered_decreased.bed $ sed 's/?/-/g' teosinte_transposed_genotypes_joined_chr4.bed | sort -k4,4nr > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr4_ordered_decreased.bed $ sed 's/?/-/g' teosinte_transposed_genotypes_joined_chr5.bed | sort -k4,4nr > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr5_ordered_decreased.bed $ sed 's/?/-/g' teosinte_transposed_genotypes_joined_chr6.bed | sort -k4,4nr > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr6_ordered_decreased.bed $ sed 's/?/-/g' teosinte_transposed_genotypes_joined_chr7.bed | sort -k4,4nr > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr7_ordered_decreased.bed $ sed 's/?/-/g' teosinte_transposed_genotypes_joined_chr9.bed | sort -k4,4nr > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr9_ordered_decreased.bed $ sed 's/?/-/g' teosinte_transposed_genotypes_joined_chr10.bed | sort -k4,4nr > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/teosinte_chr10_ordered_decreased.bed ###maize: $ sort -k3,3 maize_transposed_genotypes_joined.bed > maize_transposed_genotypes_joined_chr.bed #sort chromosome column $ sed -n '1,155p' maize_transposed_genotypes_joined_chr.bed > maize_transposed_genotypes_joined_chr1.bed $ sed -n '156,208p' maize_transposed_genotypes_joined_chr.bed > maize_transposed_genotypes_joined_chr10.bed $ sed -n '209,335p' maize_transposed_genotypes_joined_chr.bed > maize_transposed_genotypes_joined_chr2.bed $ sed -n '336,442p' maize_transposed_genotypes_joined_chr.bed > maize_transposed_genotypes_joined_chr3.bed $ sed -n '443,533p' maize_transposed_genotypes_joined_chr.bed > maize_transposed_genotypes_joined_chr4.bed $ sed -n '534,655p' maize_transposed_genotypes_joined_chr.bed > maize_transposed_genotypes_joined_chr5.bed $ sed -n '656,731p' maize_transposed_genotypes_joined_chr.bed > maize_transposed_genotypes_joined_chr6.bed $ sed -n '732,828p' maize_transposed_genotypes_joined_chr.bed > maize_transposed_genotypes_joined_chr7.bed $ sed -n '829,890p' maize_transposed_genotypes_joined_chr.bed > maize_transposed_genotypes_joined_chr8.bed $ sed -n '891,950p' maize_transposed_genotypes_joined_chr.bed > maize_transposed_genotypes_joined_chr9.bed

$ sed -n '951,956p' maize_transposed_genotypes_joined_chr.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_transposed_genotypes_joined_mutiple.bed $ sed -n '957,983p' maize_transposed_genotypes_joined_chr.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_transposed_genotypes_joined_unknown.bed

###maize: increasing position values and with missing data encoded by "-" $ sort -k4,4V maize_transposed_genotypes_joined_chr9.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr9_ordered_increased.bed #ordered based on increasing position values and with missing data encoded by "?" $ sort -k4,4V maize_transposed_genotypes_joined_chr8.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr8_ordered_increased.bed $ sort -k4,4V maize_transposed_genotypes_joined_chr7.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr7_ordered_increased.bed $ sort -k4,4V maize_transposed_genotypes_joined_chr6.bed >/home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr6_ordered_increased.bed $ sort -k4,4V maize_transposed_genotypes_joined_chr5.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr5_ordered_increased.bed $ sort -k4,4V maize_transposed_genotypes_joined_chr4.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr4_ordered_increased.bed $ sort -k4,4V maize_transposed_genotypes_joined_chr3.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr3_ordered_increased.bed $ sort -k4,4V maize_transposed_genotypes_joined_chr2.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr2_ordered_increased.bed $ sort -k4,4V maize_transposed_genotypes_joined_chr1.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr1_ordered_increased.bed $ sort -k4,4V maize_transposed_genotypes_joined_chr10.bed > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr10_ordered_increased.bed

###maize: decreasing position values and with missing data encoded by "-" $ sed 's/?/-/g' maize_transposed_genotypes_joined_chr8.bed | sort -k4,4nr > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr8_ordered_decreased.bed $ sed 's/?/-/g' maize_transposed_genotypes_joined_chr1.bed | sort -k4,4nr > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr1_ordered_decreased.bed $ sed 's/?/-/g' maize_transposed_genotypes_joined_chr2.bed | sort -k4,4nr > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr2_ordered_decreased.bed $ sed 's/?/-/g' maize_transposed_genotypes_joined_chr3.bed | sort -k4,4nr > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr3_ordered_decreased.bed $ sed 's/?/-/g' maize_transposed_genotypes_joined_chr4.bed | sort -k4,4nr > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr4_ordered_decreased.bed $ sed 's/?/-/g' maize_transposed_genotypes_joined_chr5.bed | sort -k4,4nr >/home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr5_ordered_decreased.bed $ sed 's/?/-/g' maize_transposed_genotypes_joined_chr6.bed | sort -k4,4nr > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr6_ordered_decreased.bed $ sed 's/?/-/g' maize_transposed_genotypes_joined_chr7.bed | sort -k4,4nr > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr7_ordered_decreased.bed $ sed 's/?/-/g' maize_transposed_genotypes_joined_chr9.bed | sort -k4,4nr >/home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr9_ordered_decreased.bed $ sed 's/?/-/g' maize_transposed_genotypes_joined_chr10.bed | sort -k4,4nr > /home/pyang19/Unix_Assignment_pyang19/Data-Processing-process/maize_chr10_ordered_decreased.bed