Shell Programming and Scripting

1. if $4 has del then the using the del to the right (whatever letter(s), the format of that line is REF=C;OBS=      --- line 3 --- OBS is a null string
2. if $4 has ins then the using del the to the right (whatever letter(s), the format of that line is REF=;OBS=ACA      --- line 4 --- REF is a null string

Gene	Accession_number	COSMIC_id	CDS_mut_syntax	AA_mut_syntax	Strand	HG19_coordinates	Amplicon_id	Insert	Target_url
SMARCB1	NM_003073.2	1002	c.118C>T	p.R40*	+	22:24133967-24133967	CHP2_SMARCB1_1	CCTCCGTATGTTCCGAGGTTCTCTGTACAAGAGATACCCCTCACTCTGGAGGCGACTAGCCACTGTGGAAGAGAGGAAGAAAATAGTTGCATCGTCACATGGTAAAAAAAC	http://www.sanger.ac.uk/perl/genetics/CGP/cosmic?action=mut_summary&id=1002
RB1	NM_000321	1042	c.2107-2A>G	p.?	+	13:49037865-49037865	CHP2_RB1_9	TACATCAATTTATTTACTAGATTATGATGTGTTCCATGTATGGCATATGCAAAGTGAAGAATATAGACCTTAAATTCAAAATCATT	http://www.sanger.ac.uk/perl/genetics/CGP/cosmic?action=mut_summary&id=1042
SMARCB1	NM_003073.2	1057	c.1148delC	p.P383fs	+	22:24176357-24176357	CHP2_SMARCB1_4	CCTTGGGAAGGGCAGCGCCCAGGCTGGGAGCTGGCCCCGACTCATTGCCCTCCCCACTCCTCTTCCAGGCGGATGAGGCGTCTTGCCAACACGGCCCCGGCCTGGTAACCAGCCCATCAGCACACGGCTCCC	http://www.sanger.ac.uk/perl/genetics/CGP/cosmic?action=mut_summary&id=1057
BRAF	NM_004333	144982	c.1797_1798insACA	p.T599_V600insT	-	7:140453137-140453138	CHP2_BRAF_2	TCAAACTGATGGGACCCACTCCATCGAGATTTCACTGTAGCTAGACCAAAATCACCTATTTTTACTGTGAGGTCTTCATGAAGAAATATATCTGAGGTGTAGTAAGTAAAGGAAAACAG	http://www.sanger.ac.uk/perl/genetics/CGP/cosmic?action=mut_summary&id=144982

chr22	24133967	24133967	c.118C>T	REF=C;OBS=T	SMARCB1
chr13	49037865	49037865	c.2107-2A>G	 REF=A;OBS=G	RB1
chr22	24176357	24176357	c.1148delC	REF=C;OBS=	SMARCB1
chr7	140453138	140453138	c.1797_1798insACA	REF;OBS=TACTACG	BRAF

awk 'BEGIN{ FS=OFS="\t" }NR>1{ split($7,a,":|-"); k="chr";  # define FS and OFS as tab, skip header, split $7 on : then - reading values in array a, set k equal to chr
          { split($4,b,">");                                # split $4 on > reading values into array b
            printf(k a[1],a[2],a[3],$4,"REF="b[1],"";"OBS="b[2],$1) }' file  # print desired output

awk 'NR>1{
                if($4 !~ /del/ && $4 !~ /ins/){
                                                REF=substr($4,index($4,">")-1,1);
                                                OBS=substr($4,index($4,">")+1,1)
                                              }
                else                          {
                                                e=$4;
                                                if($4 ~ /ins/){
                                                                sub(/.*ins/,"",e);
                                                                REF="";
                                                                OBS=e
                                                              };
                                                if($4 ~ /del/){
                                                                sub(/.*del/,"",e);
                                                                REF=e;
                                                                OBS=""
                                                              }
                                              };
                CHR=substr($7,1,index($7,":")-1);
                CHR_1=substr($7,index($7,":")+1,index($7,"-")-4);
                CHR_2=substr($7,index($7,"-")+1);
                if($4 !~ /ins/)               {
                                                print "chr"CHR,CHR_1 CHR_2$4,"REF="REF,"OBS="OBS,$1
                                              }
                else                          {
                                                print "chr"CHR,CHR_1,CHR_2,$4,"REF="REF,"OBS="OBS,$1
                                              }
         }
    '    Input_file

awk -F'\t' -v OFS="\t" 'NR>1{                     # define FS and OFS as tab and skip header, and start block
                if($4 !~ /del/ && $4 !~ /ins/){   # if $4 not equal to del or ins then  (start processing)
                                                REF=substr($4,index($4,">")-1,1); # extract the value to the left of the > as REF (why -1,1)?
                                                OBS=substr($4,index($4,">")+1,1)  # extract the value to the right of the > as OBS (why +1,1)?
                                              }  # end block
                else                          {  # start block
                                                e=$4                              # set $4 to e
                                                if($4 ~ /ins/){                   # if pattern ins, start block
                                                                sub(/.*ins/,"",e);  # not quite sure, is this creting an pattern index for ins
                                                                REF="";             # where REF is null
                                                                OBS=e               # and OBS is whatever the value is
                                                              };                    # end block
                                                if($4 ~ /del/){                     # if pattern del and start block
                                                                sub(/.*del/,"",e);  # not quite sure, is this creting an pattern index for del
                                                                REF=e;              # where OBS is whatever the value is
                                                                OBS=""              # and OBS is null
                                                              }                     # end block
                                              };                                    # end block
                CHR=substr($7,1,index($7,":")-1);  # split $7 on : and store value to left as CHR
                CHR_1=substr($7,index($7,":")+1,index($7,"-")-4);  # split $7 on - and store value to left as CHR_1 (why are two index needed)?
                CHR_2=substr($7,index($7,"-")+1);                  # split $7 on - and store value to right as CHR_2 (why are two index needed)?
                if($4 !~ /ins/)               {  # print output for > ($4 not equal ins and start block
                                                print "chr"CHR,CHR_1,CHR_2,$4,"REF="REF";""OBS="OBS,$1
                                              } # close block
                else                          { # start block
                                                print "chr"CHR,CHR_1,CHR_2,$4,"REF="REF";""OBS="OBS,$1  # print output if $4 has del or ins in it (set by the pattern if statements) 
                                              }  # close block
         }  # end processing
    ' input   # define input

awk 'NR>1{ ###checking here if line number is greater than 1 here, if yes then perform following steps.
                if($4 !~ /del/ && $4 !~ /ins/){ ###Checking here if 4th field is NOT having del and ins strings in them.
                                                REF=substr($4,index($4,">")-1,1); ###creating variable REF which is a substring starting from index of char > -1 to 1 character.
                                                OBS=substr($4,index($4,">")+1,1) ###creating variable OBS which is having substring of 4th field whose starting index is the index number of > +1 to till 1 character.
                                              }
                else                          { ###If a line does not have ins and del strings within them then perform following actions.
                                                e=$4; ###creating a variable named e whose value is 4th field.
                                                if($4 ~ /ins/){ ###checking if 4th field has ins string in it.
                                                                sub(/.*ins/,"",e); ###substituting all characters from starting to till ins string with NULL in e variable.
                                                                REF=""; ###Making variable REF to NULL.
                                                                OBS=e ###Making variable named OBS to new value of variable e now.
                                                              };
                                                if($4 ~ /del/){ ###Checking here if any 4th field has string del in it.
                                                                sub(/.*del/,"",e); ###substituting all characters from starting to till string del with NULL in variable named e.
                                                                REF=e; ###creating variable REF to new value of variable e here.
                                                                OBS="" ###creating OBS variable with NULL value.
                                                              }
                                              };
                CHR=substr($7,1,index($7,":")-1); ###creating variable CHR with substring whose starting point is 1st position to till index of colons index -1.
                CHR_1=substr($7,index($7,":")+1,index($7,"-")-4);### creating variable named CHR_1 with a substring whose starting point is index of colon +1 till index of dash -4 value in 7th field.
                CHR_2=substr($7,index($7,"-")+1);### creating a variable named CHR_2 here whose value is substring whose starting point is index of dash value +1 till the end of 7th field value.
                if($4 !~ /ins/)               { ###Checking if 4th field does not have ins string in it, if yes then perform following.
                                                print "chr"CHR,CHR_1 CHR_2$4,"REF="REF,"OBS="OBS,$1  ###printing values of variables CHR,CHR_1,CHR_2 etc.
                                              }
                else                          { ###Checking if 4th field does not have ins value in it, then perform following.
                                                print "chr"CHR,CHR_1,CHR_2,$4,"REF="REF,"OBS="OBS,$1 ###print the value of variables CHR,CHR_1,CHR_2 etc.
                                              }
         }
    ' Input_file                                ###Mentioning the Input_file name here.