Friday, May 27, 2022

[SOLVED] using grep (or awk) to extract two consecutive words

Issue

I have a BAM file from which I need to extract the two words starting with "PL:Z...", followed by "PR:Z..."

I started trying with the first word, but no luck :

samtools view -h file1.bam |  grep -o '\<PR[[:alnum:]]+\>'

Extracting columns with awk would have been easier, however, I observed that the column numbers for PL and PR are not consistent for all the lines in the file

 awk -v OFS='\t' '{print $21, $22}'

Test file with first 3 lines:

MN01111:72:000H3TTKV:1:13108:10015:1913 2689    SL3.0ch00       8990677 0       59H40M52H       SL3.0ch01       5122725 0    TTTTTTTTTTTTTTATTATTTTTTTTTATTTTTTTTTTTT AFFFF/FF/FFFF//FF////A/FFFF///F/FF////F/        NM:i:2  MD:Z:5A24A9     MC:Z:122M29H AS:i:30  XS:i:28 SA:Z:SL3.0ch09,55182541,-,78S31M42S,0,0;        XA:Z:SL3.0ch05,+4984944,78S33M40S,1;SL3.0ch09,-70510420,47S27M77S,0;SL3.0ch02,-52101716,44S37M70S,2;SL3.0ch08,+62573290,63S25M63S,0;  bl:Z:CGATGT     br:Z:TTTGTC     bm:Z:0  PL:Z:SL3.0ch01_5122724_5122846_FW     PR:Z:None       RG:Z:000H3TTKV_1_BSPT19472_0
MN01111:72:000H3TTKV:1:23103:5003:15527 641     SL3.0ch00       8990677 19      67S40M44S       SL3.0ch01       838549  0    CCGCTCCCCCGATCCCTTCCACCCGGTCCTTATTTTTTTTTTTTTTTTTTTTTTTTTTTATATTTTTTTTTTATTTTTTTTATTATTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTCTTTTATATTTTTGCCC        ////////6=///=///////==////////F=//FA/F/F/6//6FFF/FFFF=/F//F///FF/FAFF///F//FFF/F/FF//FF/FAAAFAFFAFA///AFFFFFF/FFAF/A///6/F///F///6/F////FF////FF///FFF       NM:i:1  MD:Z:30A9       MC:Z:105S35M11S AS:i:35 XS:i:31 SA:Z:SL3.0ch02,46044972,+,28S31M92S,0,0;      XA:Z:SL3.0ch09,-70510416,35S31M85S,0;   bl:Z:ATCACG     br:Z:GTGCCT     bm:Z:0  PL:Z:SL3.0ch05_3501697_3501846_FW     PR:Z:None       RG:Z:000H3TTKV_1_Fimande_0
MN01111:72:000H3TTKV:1:23110:15540:17389        2689    SL3.0ch00       8990677 0       10H40M101H      SL3.0ch02       39003136      0       TTTTTTTTTTTTTTTTTATTTTTTTTTATTATTTTTTTTT        F==AFFFA6FAF//F////A/F/F=///////////A/FA        NM:i:2  MD:Z:5A8A25   MC:Z:151M       AS:i:30 XS:i:29 SA:Z:SL3.0ch03,30054271,+,44S32M75S,0,0;SL3.0ch12,17846152,-,40S30M81S,0,0;     bl:Z:ATCACG   br:Z:ACCATG     bm:Z:0  PL:Z:SL3.0ch02_39003135_39003329_FW     PR:Z:None       RG:Z:000H3TTKV_1_Martyvel_0

Expected output:

PL:Z:SL3.0ch01_5122724_5122846_FW     PR:Z:None
PL:Z:SL3.0ch05_3501697_3501846_FW     PR:Z:None
PL:Z:SL3.0ch02_39003135_39003329_FW     PR:Z:None

Solution

You may use this awk that loops through all the fields and matches a field using regular expression ^P[LR]:Z: and appends it into a variable to print it in the end.

awk -v OFS='\t' '
{
   s = ""
   for (i=1; i<=NF; ++i)
      if ($i ~ /^P[LR]:Z:/)
         s = (s ? s OFS : "") $i
   print s
}' file

PL:Z:SL3.0ch01_5122724_5122846_FW   PR:Z:None
PL:Z:SL3.0ch05_3501697_3501846_FW   PR:Z:None
PL:Z:SL3.0ch02_39003135_39003329_FW PR:Z:None


Answered By - anubhava
Answer Checked By - Katrina (WPSolving Volunteer)
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