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Top Forums Shell Programming and Scripting awk to combine lines if fields match in lines Post 302997472 by cmccabe on Sunday 14th of May 2017 12:10:18 PM
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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JOIN(1) 						      General Commands Manual							   JOIN(1)

NAME
join - relational database operator SYNOPSIS
join [ options ] file1 file2 DESCRIPTION
Join forms, on the standard output, a join of the two relations specified by the lines of file1 and file2. If one of the file names is the standard input is used. File1 and file2 must be sorted in increasing ASCII collating sequence on the fields on which they are to be joined, normally the first in each line. There is one line in the output for each pair of lines in file1 and file2 that have identical join fields. The output line normally con- sists of the common field, then the rest of the line from file1, then the rest of the line from file2. Input fields are normally separated spaces or tabs; output fields by space. In this case, multiple separators count as one, and leading separators are discarded. The following options are recognized, with POSIX syntax. -a n In addition to the normal output, produce a line for each unpairable line in file n, where n is 1 or 2. -v n Like -a, omitting output for paired lines. -e s Replace empty output fields by string s. -1 m -2 m Join on the mth field of file1 or file2. -jn m Archaic equivalent for -n m. -ofields Each output line comprises the designated fields. The comma-separated field designators are either 0, meaning the join field, or have the form n.m, where n is a file number and m is a field number. Archaic usage allows separate arguments for field designators. -tc Use character c as the only separator (tab character) on input and output. Every appearance of c in a line is significant. EXAMPLES
sort /etc/passwd | join -t: -1 1 -a 1 -e "" - bdays Add birthdays to the /etc/passwd file, leaving unknown birthdays empty. The layout of /adm/users is given in passwd(5); bdays con- tains sorted lines like tr : ' ' </etc/passwd | sort -k 3 3 >temp join -1 3 -2 3 -o 1.1,2.1 temp temp | awk '$1 < $2' Print all pairs of users with identical userids. SOURCE
/src/cmd/join.c SEE ALSO
sort(1), comm(1), awk(1) BUGS
With default field separation, the collating sequence is that of sort -b -ky,y; with -t, the sequence is that of sort -tx -ky,y. One of the files must be randomly accessible. JOIN(1)
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