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awk to combine lines if fields match in lines


 
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# 1  
Old 05-12-2017
awk to combine lines if fields match in lines

In the awk below, what I am attempting to do is check each line in the tab-delimeted input, which has ~20 lines in it, for a keyword
SVTYPE=Fusion. If the keyword is found I am splitting $3 using the . (dot) and reading the portion before and after the dot in an array a.
If it does have that keyword is in line 1 then the it will also be in the line directly below it will (always and in the same location/format). The same process is performed on that
line except the split is read into array b.
Then if array b matches array a the desired output is printed tab-delimeted.
If the line does not have the word in it then that line is skipped and appears as-is in the output (nothing needs to be done to it, but it is printed in the output). I hope the awk is close, I included comments as to what I think is happening in each line. The two lines in bold and the two lines in italics should produce the desired output, the ones in color do not match and can be skipped.Thank you Smilie.

input
Code:
chr12    12006495    ETV6-NTRK3.E4N15.COSF823.1_1    G    G]chr15:88483984]    .    PASS    SVTYPE=Fusion;READ_COUNT=1868;GENE_NAME=ETV6;EXON_NUM=4;RPM=1.5825e-09;NORM_COUNT=0.001582480886121524;ANNOTATION=COSF823;FUNC=[{'gene':'ETV6','exon':'4','oncomineGeneClass':'Gain-of-Function','oncomineVariantClass':'Fusion'}]    GT:GQ    ./.:.
chr15    88483984    ETV6-NTRK3.E4N15.COSF823.1_2    T    ]chr12:12006495]T    .    PASS    SVTYPE=Fusion;READ_COUNT=1868;GENE_NAME=NTRK3;EXON_NUM=15;RPM=1.5825e-09;NORM_COUNT=0.001582480886121524;ANNOTATION=COSF823;FUNC=[{'gene':'NTRK3','exon':'15','oncomineGeneClass':'Gain-of-Function','oncomineVariantClass':'Fusion'}]    GT:GQ    ./.:.
chr12    12022903    ETV6-NTRK3.E5N15.COSF571.1_1    G    G]chr15:88483984]    .    PASS    SVTYPE=Fusion;READ_COUNT=414833;GENE_NAME=ETV6;EXON_NUM=5;RPM=3.5143e-07;NORM_COUNT=0.3514268166126607;ANNOTATION=COSF571;FUNC=[{'gene':'ETV6','exon':'5','oncomineGeneClass':'Gain-of-Function','oncomineVariantClass':'Fusion'}]    GT:GQ    ./.:.
chr15    88483984    ETV6-NTRK3.E5N15.COSF571.1_2    T    ]chr12:12022903]T    .    PASS    SVTYPE=Fusion;READ_COUNT=414833;GENE_NAME=NTRK3;EXON_NUM=15;RPM=3.5143e-07;NORM_COUNT=0.3514268166126607;ANNOTATION=COSF571;FUNC=[{'gene':'NTRK3','exon':'15','oncomineGeneClass':'Gain-of-Function','oncomineVariantClass':'Fusion'}]    GT:GQ    ./.:.
chr17    7577108    COSM10749;COSM43737    C    A,T    149.594    PASS    AF=0.0830415,0.0;AO=372,2;DP=4420;FAO=166,0;FDP=1999;FR=.,.,REALIGNEDx0.0865;FRO=1833;FSAF=82,0;FSAR=84,0;FSRF=952;FSRR=881;FWDB=0.0072184,-0.0207142;FXX=4.99998E-4;HRUN=1,1;LEN=1,1;MLLD=293.795,80.5366;OALT=A,T;OID=COSM10749,COSM43737;OMAPALT=A,T;OPOS=7577108,7577108;OREF=C,C;PB=.,.;PBP=.,.;QD=0.299338;RBI=0.00721997,0.02565;REFB=1.40155E-4,-7.81395E-4;REVB=1.50579E-4,0.0151276;RO=4043;SAF=187,1;SAR=185,1;SRF=2118;SRR=1925;SSEN=0,0;SSEP=0,0;SSSB=-0.0251826,-5.12306E-4;STB=0.52327,0.5;STBP=0.541,1.0;TYPE=snp,snp;VARB=-0.00153404,0.0;HS;FUNC=[{'origPos':'7577108','origRef':'C','normalizedRef':'C','gene':'TP53','normalizedPos':'7577108','normalizedAlt':'A','polyphen':'1.0','gt':'pos','codon':'TTT','coding':'c.830G>T','sift':'0.0','grantham':'205.0','transcript':'NM_000546.5','function':'missense','protein':'p.Cys277Phe','location':'exonic','origAlt':'A','exon':'8','oncomineGeneClass':'Loss-of-Function','oncomineVariantClass':'Hotspot'}]    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT    0/1:149:4420:1999:4043:1833:372,2:166,0:0.0830415,0.0:185,1:187,1:2118:1925:84,0:82,0:952:881:1
chr10    89624278    .    G    T    62.8836    PASS    AF=0.0785393;AO=297;DP=4155;FAO=157;FDP=1999;FR=.;FRO=1842;FSAF=77;FSAR=80;FSRF=908;FSRR=934;FWDB=0.0113997;FXX=4.99998E-4;HRUN=1;LEN=1;MLLD=117.237;OALT=T;OID=.;OMAPALT=T;OPOS=89624278;OREF=G;PB=.;PBP=.;QD=0.12583;RBI=0.040843;REFB=5.39678E-4;REVB=-0.0392199;RO=3844;SAF=150;SAR=147;SRF=1936;SRR=1908;SSEN=0;SSEP=0;SSSB=0.00159791;STB=0.502301;STBP=0.96;TYPE=snp;VARB=-0.00676678;FUNC=[{'origPos':'89624278','origRef':'G','normalizedRef':'G','gene':'PTEN','normalizedPos':'89624278','normalizedAlt':'T','gt':'pos','codon':'TAG','coding':'c.52G>T','transcript':'NM_000314.4','function':'nonsense','protein':'p.Glu18Ter','location':'exonic','origAlt':'T','exon':'1'}]    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT    0/1:62:4155:1999:3844:1842:297:157:0.0785393:147:150:1936:1908:80:77:908:934:1

awk with comments

Code:
awk -F'\t' -v OFS="\t"' # call awk and set FS and OFS as tab
{
match($0,/SVTYPE=[^;]*/); # look in line for SVTYPE
SVTYPE_VALUE=substr($0,RSTART+7,RLENGTH-7); # index SVTYPE for Fusion (value to look for)
if(SVTYPE_VALUE == "Fusion"){ # if SVTYPE is Fusion
{split($3,a,"."); a=a[1]"."a[2]}' # split the string in $3 at using the . and store the portion before the . and after (ETV6-NTRK3.E4N15) in array
a else if(SVTYPE_VALUE !~ "Fusion") # if SVTYPE not Fusion
next; # skip to next line
}
}
}
{
match($0,/SVTYPE=[^;]*/); # look in line for SVTYPE
SVTYPE_VALUE=substr($0,RSTART+7,RLENGTH-7); # index SVTYPE for Fusion (value to look for)
if(SVTYPE_VALUE == "Fusion"){ # if SVTYPE is Fusion
{split($3,b,"."); b=b[1]"."b[2]}' # split the string in $3 at using the . and store the portion before the . and after (ETV6-NTRK3.E4N15) in array
b else if(SVTYPE_VALUE !~ "Fusion") # if SVTYPE not Fusion
next; # skip to next line
} 
} 
}
} 
} 
}
{
for(j in b){ # define loop
for(i=1;i<=length(a);i++){ # iterate through loop
if(b[j] ~ a[i]){ # compare array b to array a for match
print --- desired output ----
}
}
}' input | awk 'BEGIN {print "Position\tLocus\tClass\tFunction\tGene\tCount"}' > output # add header

desired output
Code:
Locus    Class    Function    Gene    Count
chr12:12006495-chr15:88483984    Fusion    Gain-of-function    ETV6E4-NTRK3E15    1868
chr12:12022903-chr15:88483984Fusion    Gain-of-function    ETV6E5-NTRK3E15    414833   
chr17    7577108    COSM10749;COSM43737    C    A,T    149.594    PASS    AF=0.0830415,0.0;AO=372,2;DP=4420;FAO=166,0;FDP=1999;FR=.,.,REALIGNEDx0.0865;FRO=1833;FSAF=82,0;FSAR=84,0;FSRF=952;FSRR=881;FWDB=0.0072184,-0.0207142;FXX=4.99998E-4;HRUN=1,1;LEN=1,1;MLLD=293.795,80.5366;OALT=A,T;OID=COSM10749,COSM43737;OMAPALT=A,T;OPOS=7577108,7577108;OREF=C,C;PB=.,.;PBP=.,.;QD=0.299338;RBI=0.00721997,0.02565;REFB=1.40155E-4,-7.81395E-4;REVB=1.50579E-4,0.0151276;RO=4043;SAF=187,1;SAR=185,1;SRF=2118;SRR=1925;SSEN=0,0;SSEP=0,0;SSSB=-0.0251826,-5.12306E-4;STB=0.52327,0.5;STBP=0.541,1.0;TYPE=snp,snp;VARB=-0.00153404,0.0;HS;FUNC=[{'origPos':'7577108','origRef':'C','normalizedRef':'C','gene':'TP53','normalizedPos':'7577108','normalizedAlt':'A','polyphen':'1.0','gt':'pos','codon':'TTT','coding':'c.830G>T','sift':'0.0','grantham':'205.0','transcript':'NM_000546.5','function':'missense','protein':'p.Cys277Phe','location':'exonic','origAlt':'A','exon':'8','oncomineGeneClass':'Loss-of-Function','oncomineVariantClass':'Hotspot'}]    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT    0/1:149:4420:1999:4043:1833:372,2:166,0:0.0830415,0.0:185,1:187,1:2118:1925:84,0:82,0:952:881:1
chr10    89624278    .    G    T    62.8836    PASS    AF=0.0785393;AO=297;DP=4155;FAO=157;FDP=1999;FR=.;FRO=1842;FSAF=77;FSAR=80;FSRF=908;FSRR=934;FWDB=0.0113997;FXX=4.99998E-4;HRUN=1;LEN=1;MLLD=117.237;OALT=T;OID=.;OMAPALT=T;OPOS=89624278;OREF=G;PB=.;PBP=.;QD=0.12583;RBI=0.040843;REFB=5.39678E-4;REVB=-0.0392199;RO=3844;SAF=150;SAR=147;SRF=1936;SRR=1908;SSEN=0;SSEP=0;SSSB=0.00159791;STB=0.502301;STBP=0.96;TYPE=snp;VARB=-0.00676678;FUNC=[{'origPos':'89624278','origRef':'G','normalizedRef':'G','gene':'PTEN','normalizedPos':'89624278','normalizedAlt':'T','gt':'pos','codon':'TAG','coding':'c.52G>T','transcript':'NM_000314.4','function':'nonsense','protein':'p.Glu18Ter','location':'exonic','origAlt':'T','exon':'1'}]    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT    0/1:62:4155:1999:3844:1842:297:157:0.0785393:147:150:1936:1908:80:77:908:934:1

description of output
Code:
header line
$1:$2 of line 1 - $1:$2 of line 2     SVTYPE=(value)     oncomineGeneClass=(value)     array a and array b match (value)     READ_Count=(value)   
lines that were nor processed


Last edited by cmccabe; 05-12-2017 at 01:43 PM.. Reason: added details and fixed format
# 2  
Old 05-12-2017
Hello cmccabe,

Could you please check if following may help you in same.
Code:
awk '/SVTYPE=Fusion/{match($5,/].*]/);sub(/.COS.*/,"",$3);sub(/-/,"",$3);sub(/\./,"-",$3);VAL=substr($5,RSTART+1,RLENGTH-2);num=split($8, array,";");for(i=1;i<=num;i++){if(array[i] ~  /SVTYPE/){sub(/.*=/,"",array[i]);svtype=array[i]};if(array[i] ~ /READ_COUNT/){sub(/.*=/,"",array[i]);read_count=array[i]}};match($0,/oncomineGeneClass.*,/);print $1":"$2 "-" VAL OFS svtype OFS substr($0,RSTART+20,RLENGTH-22) OFS $3 OFS read_count;}'  Input_file

EDIT: Adding a non-one liner form of solution too now.
Code:
awk '/SVTYPE=Fusion/{
                        match($5,/].*]/);
                        sub(/.COS.*/,"",$3);
                        sub(/-/,"",$3);
                        sub(/\./,"-",$3);
                        VAL=substr($5,RSTART+1,RLENGTH-2);
                        num=split($8, array,";");
                        for(i=1;i<=num;i++){
                                                if(array[i] ~  /SVTYPE/){
                                                sub(/.*=/,"",array[i]);
                                                svtype=array[i]
                                                                        };
                                                if(array[i] ~ /READ_COUNT/){
                                                sub(/.*=/,"",array[i]);
                                                read_count=array[i]
                                                                           }
                                           };
                        match($0,/oncomineGeneClass.*,/);
                        print $1":"$2 "-" VAL OFS svtype OFS substr($0,RSTART+20,RLENGTH-22) OFS $3 OFS read_count;
                    }
    '   Input_file

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
# 3  
Old 05-12-2017
The output is very close, but only line 1 and 3 are printed because line 2 matches 1 and line 4 matches 3.

output of script
Code:
 chr12:12006495-chr15:88483984 Fusion Gain-of-Function ETV6NTRK3-E4N15 1868
chr15:88483984-chr12:12006495 Fusion Gain-of-Function ETV6NTRK3-E4N15 1868
chr12:12022903-chr15:88483984 Fusion Gain-of-Function ETV6NTRK3-E5N15 414833
chr15:88483984-chr12:12022903 Fusion Gain-of-Function ETV6NTRK3-E5N15 414833

desired output
Code:
 chr12:12006495-chr15:88483984 Fusion Gain-of-Function ETV6NTRK3-E4N15 1868
 chr12:12022903-chr15:88483984 Fusion Gain-of-Function ETV6NTRK3-E5N15 414833
 chr17 entire line.... (this line does not have the keyword in it so is printed in the output)
 chr10 entire line...   (this line does not have the keyword in it so is printed in the output

Would you be able to comment each line so I may better understand? Thank you very much Smilie.

Code:
awk '/SVTYPE=Fusion/{   # regex to look in line for SVTYPE=Fusion
                        match($5,/].*]/);  # grab the $5 value after the ] but before theouter ] (chr15:88483984)
                        sub(/.COS.*/,"",$3);  # split on the . before COS and grag the value in $3 (ETV6-NTRK3.E4N15)
                        sub(/-/,"",$3);   # split on the - and grab the text to the left (ETV6) 
                        sub(/\./,"-",$3);   # split on the - and grab the text to the right and add a hypen before (-NTRK3)
                        VAL=substr($5,RSTART+1,RLENGTH-2);    # not sure haven't got the concept of RSTART and RLENGTH
                        num=split($8, array,";");  # read the $8 value into array up to the ; (SVTYPE=Fusion}
                        for(i=1;i<=num;i++){  # create loop to iterate next line
                                                if(array[i] ~  /SVTYPE/){ # check array 
                                                sub(/.*=/,"",array[i]);    # matches in next line
                                                svtype=array[i]  # define match criteria
                                                                        };
                                                if(array[i] ~ /READ_COUNT/){   #  strore value of READ_COUNT in array[i] 
                                                sub(/.*=/,"",array[i]);   #  value of READ_COUNT in array[i] (1868)
                                                read_count=array[i]    # define match and print to line
                                                                           }
                                           }; 
                        match($0,/oncomineGeneClass.*,/);  # grab(Gain-of-function
                        print $1":"$2 "-" VAL OFS svtype OFS substr($0,RSTART+20,RLENGTH-22) OFS $3 OFS read_count;  # print desired output
                    }
    '   Input_file

I do not really understand RSTART and RLENGTH fully but believe they define the index of a field.

Last edited by cmccabe; 05-12-2017 at 08:29 PM.. Reason: added comments to code as what I think I understand
# 4  
Old 05-13-2017
Hello cmccabe,

Could you please go through following and let me know if this helps you.
Code:
awk '/SVTYPE=Fusion/{                                                                                                 #### Searching the string SVTYPE=Fusion on each line. If it is found then perform following actions.
                        match($5,/].*]/);                                                                             #### Using match functionality by providing the regex where it will match from ] to till ] in 5th field.
                        sub(/.COS.*/,"",$3);                                                                          #### Substituting the .COS.* means from .COS to everything to NULL in 3rd field.
                        sub(/-/,"",$3);                                                                               #### Substituting -(dash) with NULL in 3rd field.
                        sub(/\./,"-",$3);                                                                             #### Substituting DOT with - in 3rd field.
                        VAL=substr($5,RSTART+1,RLENGTH-2);                                                            #### Putting the values of subtring whose value starts from RSTART+1 to RLENGTH-2, here point to be noted RSTART and RLENGTH are the OOTB awk's keywords which will be SET when a match is found, we have done this match for 5th field above.
                        num=split($8, array,";");                                                                     #### Splitting field 8th whose delimiter is ";" and storing it's length(array's length) to variable named num. 
                        for(i=1;i<=num;i++){                                                                          #### Starting a loop which will start from value 1 of variable i to till value of variable num.
                                                if(array[i] ~  /SVTYPE/){                                             #### Checking here condition if any array's value is equal to /SVTYPE/ then do following.
                                                sub(/.*=/,"",array[i]);                                               #### If above condition is TRUE then substituting the .*= everything till = to NULL in array[i]'s value.
                                                svtype=array[i];                                                      #### Keeping array[i]'s value in variable named svtype.
                                                                        };
                                                if(array[i] ~ /READ_COUNT/){                                          #### Checking another condition where checking if array a's value is equal to /READ_COUNT/ then perform following actions.
                                                sub(/.*=/,"",array[i]);                                               #### substituting everything till = to NULL in array[i]'s value.
                                                read_count=array[i]                                                   #### Storing value of array[i]'s in read_count.
                                                                           }
                                           };
                        match($0,/oncomineGeneClass.*,/);                                                             #### Using match function of awk to perform a match from  /oncomineGeneClass.*/ here.
                        print $1":"$2 "-" VAL OFS svtype OFS substr($0,RSTART+20,RLENGTH-22) OFS $3 OFS read_count;   #### printing the values of $1, $2, VAL(which is having the values of 1st match which we performed above for $5), svtype, subtring of above used match for /oncomineGeneClass.* then read_count values.
                    }
    '   Input_file                                                                                                    #### Mentioning the Input_file.

NOTE: Kindly DO NOT run the above code it is only for explanation purposes.

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
# 5  
Old 05-14-2017
I have added two lines to add a header and remove duplicates based on $4. The portion of code in bold below was an attempt to print the two lines (in this example, there may be more). If the SVTYPE=Fusion is not true then the entire line is printed in the output. Thank you Smilie.

Code:
awk -v OFS="\t" '/SVTYPE=Fusion/{
                        match($5,/].*]/);
                        sub(/.COS.*/,"",$3);
                        sub(/-/,"",$3);
                        sub(/\./,"-",$3);
                        VAL=substr($5,RSTART+1,RLENGTH-2);
                        num=split($8, array,";");
                        for(i=1;i<=num;i++){
                                                if(array[i] ~  /SVTYPE/){
                                                sub(/.*=/,"",array[i]);
                                                svtype=array[i]
                                                         
               };
                                                if(array[i] ~ /READ_COUNT/){
                                                sub(/.*=/,"",array[i]);
                                                read_count=array[i]
                                                                           }
                                           };
                        match($0,/oncomineGeneClass.*,/);
                        print "Locus\tType\tFunction\tGene\tReads" ### add header
                        print $1":"$2 "-" VAL OFS svtype OFS substr($0,RSTART+20,RLENGTH-22) OFS $3 OFS read_count;
                        ' $8 != "\"SVTYPE=Fusion\"" {print;}'
                    }
' input | awk -F'\t' '!seen[$4]++'### remove duplicates based on $4

awk: cmd. line:21:                         
awk: cmd. line:21:                         ^ unexpected newline or end of string

current output
Code:
chr12:12006495-chr15:88483984 Fusion Gain-of-Function ETV6NTRK3-E4N15 1868
chr12:12022903-chr15:88483984 Fusion Gain-of-Function ETV6NTRK3-E5N15 414833

desired output
Code:
chr12:12006495-chr15:88483984 Fusion Gain-of-Function ETV6NTRK3-E4N15 1868
chr12:12022903-chr15:88483984 Fusion Gain-of-Function ETV6NTRK3-E5N15 414833
chr17 entire line.... (this line does not have the keyword in it so is printed in the output)
chr10 entire line...   (this line does not have the keyword in it so is printed in the output


Last edited by cmccabe; 05-14-2017 at 11:48 AM.. Reason: added current output
# 6  
Old 05-14-2017
Hello cmccabe,

If you simply want to print the lines which doesn't have condition of string fusion then following may help you in same(I haven't tested it though).
Code:
awk '/SVTYPE=Fusion/{
                        match($5,/].*]/);
                        sub(/.COS.*/,"",$3);
                        sub(/-/,"",$3);
                        sub(/\./,"-",$3);
                        VAL=substr($5,RSTART+1,RLENGTH-2);
                        num=split($8, array,";");
                        for(i=1;i<=num;i++){
                                                if(array[i] ~  /SVTYPE/){
                                                sub(/.*=/,"",array[i]);
                                                svtype=array[i]
                                                                        };
                                                if(array[i] ~ /READ_COUNT/){
                                                sub(/.*=/,"",array[i]);
                                                read_count=array[i]
                                                                           }
                                           };
                        match($0,/oncomineGeneClass.*,/);
                        print $1":"$2 "-" VAL OFS svtype OFS substr($0,RSTART+20,RLENGTH-22) OFS $3 OFS read_count;
			next
                    }
    1
    '   Input_file

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
# 7  
Old 05-14-2017
The output seems to be only 3 of the 4 lines (in this example there are 4 lines, but that is variable depending on the input.
Is the next only processing one of the lines because they both do not have SVTYPE=Fusion so it only sees one line?. Thank you Smilie.

Code:
Locus    Type    Function    Gene    Reads
chr12:12006495-chr15:88483984    Fusion    Gain-of-Function    ETV6NTRK3-E4N15    1868
chr12:12022903-chr15:88483984    Fusion    Gain-of-Function    ETV6NTRK3-E5N15    414833
chr17    7577108    COSM10749;COSM43737    C    A,T    149.594    PASS    AF=0.0830415,0.0;AO=372,2;DP=4420;FAO=166,0;FDP=1999;FR=.,.,REALIGNEDx0.0865;FRO=1833;FSAF=82,0;FSAR=84,0;FSRF=952;FSRR=881;FWDB=0.0072184,-0.0207142;FXX=4.99998E-4;HRUN=1,1;LEN=1,1;MLLD=293.795,80.5366;OALT=A,T;OID=COSM10749,COSM43737;OMAPALT=A,T;OPOS=7577108,7577108;OREF=C,C;PB=.,.;PBP=.,.;QD=0.299338;RBI=0.00721997,0.02565;REFB=1.40155E-4,-7.81395E-4;REVB=1.50579E-4,0.0151276;RO=4043;SAF=187,1;SAR=185,1;SRF=2118;SRR=1925;SSEN=0,0;SSEP=0,0;SSSB=-0.0251826,-5.12306E-4;STB=0.52327,0.5;STBP=0.541,1.0;TYPE=snp,snp;VARB=-0.00153404,0.0;HS;FUNC=[{'origPos':'7577108','origRef':'C','normalizedRef':'C','gene':'TP53','normalizedPos':'7577108','normalizedAlt':'A','polyphen':'1.0','gt':'pos','codon':'TTT','coding':'c.830G>T','sift':'0.0','grantham':'205.0','transcript':'NM_000546.5','function':'missense','protein':'p.Cys277Phe','location':'exonic','origAlt':'A','exon':'8','oncomineGeneClass':'Loss-of-Function','oncomineVariantClass':'Hotspot'}]    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT    0/1:149:4420:1999:4043:1833:372,2:166,0:0.0830415,0.0:185,1:187,1:2118:1925:84,0:82,0:952:881:1


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1. Shell Programming and Scripting

awk to remove lines that do not start with digit and combine line or lines

I have been searching and trying to come up with an awk that will perform the following on a converted text file (original is a pdf). 1. Since the first two lines are (begin with) text they are removed 2. if $1 is a number then all text is merged (combined) into one line until the next... (3 Replies)
Discussion started by: cmccabe
3 Replies

2. Shell Programming and Scripting

awk to combine matching lines in file

I am trying to combine all matching lines in the tab-delimited using awk. The below runs but no output results. Thank you :). input chrX 110925349 110925532 ALG13 chrX 110925349 110925532 ALG13 chrX 110925349 110925532 ALG13 chrX 47433390 47433999 SYN1... (3 Replies)
Discussion started by: cmccabe
3 Replies

3. UNIX for Beginners Questions & Answers

How to count lines of CSV file where 2 fields match variables?

I'm trying to use awk to count the occurrences of two matching fields of a CSV file. For instance, for data that looks like this... Joe,Blue,Yes,No,High Mike,Blue,Yes,Yes,Low Joe,Red,No,No,Low Joe,Red,Yes,Yes,Low I've been trying to use code like this... countvar=`awk ' $2~/$color/... (4 Replies)
Discussion started by: nmoore2843
4 Replies

4. Shell Programming and Scripting

awk to combine lines from line with pattern match to a line that ends in a pattern

I am trying to combine lines with these conditions: 1. First line starts with text of "libname VALUE db2 datasrc" where VALUE can be any text. 2. If condition1 is met then continue to combine lines through a line that ends with a semicolon. 3. Ignore case when matching patterns and remove any... (5 Replies)
Discussion started by: Wes Kem
5 Replies

5. Shell Programming and Scripting

Awk: Combine multiple lines based on number of fields

If a file has following kind of data, comma delimited 1,2,3,4 1 1 1,2,3,4 1,2 2 2,3,4 My required output must have only 4 columns with comma delimited 1,2,3,4 111,2,3,4 1,222,3,4 I have tried many awk command using ORS="" but couldnt progress (10 Replies)
Discussion started by: mdkm
10 Replies

6. UNIX for Dummies Questions & Answers

awk - (URGENT!) Print lines sort and move lines if match found

URGENT HELP IS NEEDED!! I am looking to move matching lines (01 - 07) from File1 and 77 tab the matching string from File2, to File3.txt. I am almost done but - Currently, script is not printing lines to File3.txt in order. - Also the matching lines are not moving out of File1.txt ... (1 Reply)
Discussion started by: High-T
1 Replies

7. Shell Programming and Scripting

Print only lines where fields concatenated match strings

Hello everyone, Maybe somebody could help me with an awk script. I have this input (field separator is comma ","): 547894982,M|N|J,U|Q|P,98,101,0,1,1 234900027,M|N|J,U|Q|P,98,101,0,1,1 234900023,M|N|J,U|Q|P,98,54,3,1,1 234900028,M|H|J,S|Q|P,98,101,0,1,1 234900030,M|N|J,U|F|P,98,101,0,1,1... (2 Replies)
Discussion started by: Ophiuchus
2 Replies

8. UNIX for Dummies Questions & Answers

awk display the match and 2 lines after the match is found.

Hello, can someone help me how to find a word and 2 lines after it and then send the output to another file. For example, here is myfile1.txt. I want to search for "Error" and 2 lines below it and send it to myfile2.txt I tried with grep -A but it's not supported on my system. I tried with awk,... (4 Replies)
Discussion started by: eurouno
4 Replies

9. Shell Programming and Scripting

search and combine lines in awk

Hi All, I have 1 "keyword" file like this: 00-1F-FB-00-04-18 00-19-CB-8E-66-DF 00-1F-FB-00-48-9C 00-1F-FB-00-AA-4F .... and the 2nd "details" file like this: Wed Feb 11 00:00:02 2009 NAS-IP-Address = xxxxxxxxxxxxxxxxxx Class = "P1-SHT-AAA01;1233704662;4886720" ... (6 Replies)
Discussion started by: xajax7
6 Replies

10. UNIX for Dummies Questions & Answers

SImple HELP! how to combine two lines together using sed or awk..

hi..im new to UNIX... ok i have this information in the normal shell... there are 2 lines display like this: h@hotmail.com k@hotmail.com i want it to display like this with a space betweem them h@hotmail.com k@hotmail.com the information is stored in a text file.... anyone... (10 Replies)
Discussion started by: forevercalz
10 Replies

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