Thank you. What does the curl do at the beginning of your code?
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Picard CollectAlignmentMetrics Output
I am confused by the output that Picard CollectAlignmentMetrics is giving me. I think it is the format.
## METRICS CLASS picard.analysis.AlignmentSummaryMetrics
CATEGORY TOTAL_READS PF_READS PCT_PF_READS PF_NOISE_READS PF_READS_ALIGNED PCT_PF_READS_ALIGNED PF_ALIGNED_BASES PF_HQ_ALIGNED_READS PF_HQ_ALIGNED_BASES PF_HQ_ALIGNED_Q20_BASES PF_HQ_MEDIAN_MISMATCHES PF_MISMATCH_RATE PF_HQ_ERROR_RATE PF_INDEL_RATE MEAN_READ_LENGTH READS_ALIGNED_IN_PAIRS PCT_READS_ALIGNED_IN_PAIRS BAD_CYCLES STRAND_BALANCE PCT_CHIMERAS PCT_ADAPTER SAMPLE LIBRARY READ_GROUP
FIRST_OF_PAIR 1000000 1000000 1 0 1000000 1 99990119 999271 99917232 99487798 0 0.003925 0.003924 0.00009100 1000000 1 0 0.50084 0 0
SECOND_OF_PAIR 1000000 1000000 1 0 1000000 1 99989751 999225 99912264 99481794 0 0.003919 0.003919 0.00009100 1000000 1 0 0.49916 0 0
PAIR 2000000 2000000 1 0 2000000 1 199979870 1998496 199829496 198969592 0 0.003922 0.003922 0.000092 100 2000000 1 0 0.5 0 0
Is there a way to format this so that it is readable?
Thanks
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Pierre Lindenbaum
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fiona.newberry
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fiona.newberry
1 answer
using awk:
curl -Ls "https://raw.githubusercontent.com/ewels/MultiQC_TestData/master/data/modules/picard/CollectMultipleMetrics/A1.sorted.dup.recal.all.metrics.alignment_summary_metrics" |\
awk '/^CATEGORY/ {split($0,header);n=1;next; } {if(n!=1) next; for(i=2;i<=NF;++i) printf("%s\t%s\t%s\n",$1,header[i],$i);}' |\
column -t
.
FIRST_OF_PAIR TOTAL_READS 48300305
FIRST_OF_PAIR PF_READS 48300305
FIRST_OF_PAIR PCT_PF_READS 1
FIRST_OF_PAIR PF_NOISE_READS 0
FIRST_OF_PAIR PF_READS_ALIGNED 48290537
FIRST_OF_PAIR PCT_PF_READS_ALIGNED 0.999798
FIRST_OF_PAIR PF_ALIGNED_BASES 6040566328
FIRST_OF_PAIR PF_HQ_ALIGNED_READS 47217927
FIRST_OF_PAIR PF_HQ_ALIGNED_BASES 5910135054
FIRST_OF_PAIR PF_HQ_ALIGNED_Q20_BASES 5804787451
FIRST_OF_PAIR PF_HQ_MEDIAN_MISMATCHES 0
FIRST_OF_PAIR PF_MISMATCH_RATE 0.00187
FIRST_OF_PAIR PF_HQ_ERROR_RATE 0.001761
FIRST_OF_PAIR PF_INDEL_RATE 0.000093
FIRST_OF_PAIR MEAN_READ_LENGTH 125.537288
FIRST_OF_PAIR READS_ALIGNED_IN_PAIRS 48246679
FIRST_OF_PAIR PCT_READS_ALIGNED_IN_PAIRS 0.999092
FIRST_OF_PAIR BAD_CYCLES 0
FIRST_OF_PAIR STRAND_BALANCE 0.44083
FIRST_OF_PAIR PCT_CHIMERAS 0.001303
FIRST_OF_PAIR PCT_ADAPTER 0.000001
SECOND_OF_PAIR TOTAL_READS 48300305
SECOND_OF_PAIR PF_READS 48300305
SECOND_OF_PAIR PCT_PF_READS 1
SECOND_OF_PAIR PF_NOISE_READS 0
SECOND_OF_PAIR PF_READS_ALIGNED 48250591
SECOND_OF_PAIR PCT_PF_READS_ALIGNED 0.998971
SECOND_OF_PAIR PF_ALIGNED_BASES 6025327891
SECOND_OF_PAIR PF_HQ_ALIGNED_READS 47170746
SECOND_OF_PAIR PF_HQ_ALIGNED_BASES 5894822755
SECOND_OF_PAIR PF_HQ_ALIGNED_Q20_BASES 5697735258
SECOND_OF_PAIR PF_HQ_MEDIAN_MISMATCHES 0
SECOND_OF_PAIR PF_MISMATCH_RATE 0.002515
SECOND_OF_PAIR PF_HQ_ERROR_RATE 0.002401
SECOND_OF_PAIR PF_INDEL_RATE 0.000097
SECOND_OF_PAIR MEAN_READ_LENGTH 125.429941
SECOND_OF_PAIR READS_ALIGNED_IN_PAIRS 48246679
SECOND_OF_PAIR PCT_READS_ALIGNED_IN_PAIRS 0.999919
SECOND_OF_PAIR BAD_CYCLES 0
SECOND_OF_PAIR STRAND_BALANCE 0.559123
SECOND_OF_PAIR PCT_CHIMERAS 0.001303
SECOND_OF_PAIR PCT_ADAPTER 0.000001
PAIR TOTAL_READS 96600610
PAIR PF_READS 96600610
PAIR PCT_PF_READS 1
PAIR PF_NOISE_READS 0
PAIR PF_READS_ALIGNED 96541128
PAIR PCT_PF_READS_ALIGNED 0.999384
PAIR PF_ALIGNED_BASES 12065894219
PAIR PF_HQ_ALIGNED_READS 94388673
PAIR PF_HQ_ALIGNED_BASES 11804957809
PAIR PF_HQ_ALIGNED_Q20_BASES 11502522709
PAIR PF_HQ_MEDIAN_MISMATCHES 0
PAIR PF_MISMATCH_RATE 0.002192
PAIR PF_HQ_ERROR_RATE 0.002081
PAIR PF_INDEL_RATE 0.000095
PAIR MEAN_READ_LENGTH 125.483615
PAIR READS_ALIGNED_IN_PAIRS 96493358
PAIR PCT_READS_ALIGNED_IN_PAIRS 0.999505
PAIR BAD_CYCLES 0
PAIR STRAND_BALANCE 0.499952
PAIR PCT_CHIMERAS 0.001303
PAIR PCT_ADAPTER 0.000001
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Pierre Lindenbaum
If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
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WouterDeCoster
curl just gets a summary file i've found on the web
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Pierre Lindenbaum
Sorry to ask another question, but I am confused as to how actually use the above command. I am new to linux. My filename is metrics.txt so would i put that at the end of the awk command?
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fiona.newberry
o would i put that at the end of the awk command
yes or just 'cat'
cat your.file.metrics |\
awk '/^CATEGORY/ {split($0,header);n=1;next; } {if(n!=1) next; for(i=2;i<=NF;++i) printf("%s\t%s\t%s\n",$1,header[i],$i);}' |\
column -t
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Pierre Lindenbaum
Another question. It does not recognise the column -t section
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fiona.newberry
Strange.. column is quite common.
but your can jyst remove the 'column -t' part. It's just here to reformat the text; or install 'column' https://unix.stackexchange.com/questions/330506/
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Pierre Lindenbaum
Thanks, it seems to be working now. Is there a way to change the format in the actual text file? Not the version printed to the terminal
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fiona.newberry
Log in to answer this question.
You can add formatting by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:
I'm not sure how the output should look like so I haven't changed your post.