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Reading file to array
$XXXX00000182183 A B C D 2336458 0.38052728 0.47743206 0.7575053 -0.6718711 2336459 0.28057157 0.15925342 1.6066561 -0.6718711 2336464 0.51131811 0.09128078 2.0090009 -0.6718711 2336466 -0.24900861 0.13113013 -1.7475722 -0.6718711 2336469 0.38724031 0.06652635... -
Overlap filter in between two file
Need help, data1 1 59851 59880 CATTCTAGTGTAAAGTTTTAGATCTTATAT 1 59881 59910 AACTGTGAGATTAATCTCAGATAATGACAC 1 59911 59940 AAAATATAGTGAAGTTGGTAAGTTATTTAG 1 59941 59970 TAAAGCTCATGAAAATTGTGCCCTCCATTC 1 59971 60000 CCATATAATTTAGTAATTGTCTAGGAACTT 1... -
sum the value in each column for repeat sequence under $1
I want to add respective column for repeat item on $1. If there is no repeat sequence on $1, I want the exact count in each col. Please would you help me guys! ---------------------------------------------------------- data Name a b c d e f g h GGGACGG 2 0 7 10 2 0 4 0 GGGAGGG 0 0 4 26 8 3 0 0... -
Format file
Would you please help me in formating the folling file. File looks like the folloing. I want to capture, The "AC" and ID row and print $2 and $3 if the file contain "hsa_" in column three. See the result file I want at the end of this file. -----------data---------------- AC MIPF0000001 ID... -
search and count
Hi guys, Is there easy way to searcha and count the following. File1 TCGTCTGCCGTTTTTT TCTCTGAGGGTCGGT File2 TCGTCTGCCGTTTTTT TCGTCTGCCGTTTTTTCCTTG TCGTCTGCCGTTTTTTCCTTTTCATCTTAAAAAAAA TCGTCTGCCGTTTTTTCGTTGGCAACAATAAAGTCT TCGTCTGCCGTTTTTTG TCGTCTGCCGTTTTTTG TCGTCTGCCGTTTTTTG... -
None overlap lines
Is there any way I can negate the following line. I want to print none-overlap lines between two files. Rather than "in a", I want "not in a" awk 'NR==FNR{a[$2","$3","$6]=$0;next}$2","$3","$6 in a{print a[$2","$3","$6]"\t"$0}' $* Thanks D -
Multiline concatination
How I can concatinate >1 AAAAAAAAAAA BBBBBBBBBBBBB CCCCCCCCCCCC To get >1 AAAAAAAAAABBBBBBBBBCCCCCCCCCCC I have tried the following and it only capture the first line and stops. awk '/^>/ {print; "\t"; getline; print}' $* -
awk monks, I am back with question
I want format the following data 1 177921 N 1 123822 G 1 116756 P 1 131946 m 2 1779 N 2 1238 G 2 1167 P 2 1319 m 3 177921 N 3 123822 G 3 116756 m I want: header1 N G P M 1 177921 123822 116756 131946 2 1779 1238 1167 1319 3 177921... -
Pattern not recoginized when set as multiline
I am getting " unterminated pattern error" while I excute the script. If I write the pattern as single line on vi editor it will work but the script will be ugly. $1~/^A|B|c|d|e|f|g|h/ THIS WILL WORK WITH OUT ANY PROBLEM If I wrote the same line as: $1~/^A|B |C|D |E|F |G|h/ I... -
Match two file using grep and awk
I want to match two file using grep and awk. Here is Data1 and Data2. I want to get overlap only if the following is true: $1(Data1)==$1(Data2) && $3(Data1)==4(Data2) Data1: I929_79_46226_x388 GCAAAGCACACGGCCTGC 10 I929_79_145232_x1 TAGCAGCGGGAACAGTTC 11 Data2: I929_79_145232_x1... -
excuting saved awk script from command line
I have a problem of feeding input file to saved awk script. I want to save awk scirpt to a file and feed the file name from command line but do not work. test.awk --------------------------------------------- awk "{$1~/query|seq/}{a[$1]=$2}{print a["query"]"\t"a["seq"]"\t"}'... -
Search string in other file
I know perl way to search a string inside other file. Is there an easy awk way to search a string in side second file? Example: Data1 1 TGAGGTAGTAGGTTGTATAGTT 2 CTATACAATCTACTGTCTTTC Exaple: Data2 >1 TGAGGTAGTAGGTTGTATAGTT >2 TGAGGTAGTAGGTTGTATAGTT >3 TGAGGTAGTAGGTTGTATAGTT >4... -
The or logic didn't work on bash
These two line didn't work on my bash! awk '{gsub(/\r/,"")}substr($0,2,15)~/\./||/^A{15}/||/^G{15}/||/^T{15}/||/^C{15}/||length($0)<14{next}1' gcb110_adaptor_removed.txt _-------------------------------------------------------- awk 'index(substr($1, 2, 10), ".")==0||index(substr($1, 1, 15)... -
Recognizing empty line using ""
The following script works when I have changed to ==1 but will not exclude when I changed to ==0. The other problem is that I want to recognize and exclude lines with shorter reads less than 14 character using index(substr($1, 1, 14), " ")==0 but will not work awk 'index(substr($1, 2, 10)... -
Practical question!!!
I want give each line a unique id. Here is the inpute data: TGAGGTATTATGTTCGAT 1 GGGGGCGACTCTGGGATG 3 CGGAGCGGGCTTCTCTTC 1 AGGGGGATGGTGGAAAAA 1 TGGCTCAGGGCAGAAGGA 2 TACTACAGGGTAGAACC 49 I want to give each line an id looks like this >xxx_1_x1 TGAGGTATTATGTTCGAT >xxx_2_x3... -
Tired of Excel filter
Hi Guys, I hope I will get solution from awk, I am tired of opening and filtering the sequence per mellion line. I want to discard a sequence if more than two . at the begening( meaning character 1-10) Data: GCGGAA.GATCATTA GCGA.GGCA.GCCG.CC. GCTCCGGGA.GGCTCGGG CTCC...A.GGCTGGGA... -
character count
Is there any simple single line command to count character in awk? I want some thing like =len(A1) in excel. input data: AAAAGCTGGGTTGAGAGGGCGA AAAAGCTGGGTTGAGAGGGCGA AAAAGCTGGGTTGAGAGGGCGA AAAAGCTGGGTTGAGAGGGCGA AAAAGCTGGGTTGAGAGGGCGA AAAAGCTGGGTTGAGAGGGCGA AAAAGCTGGGTTGAGAGGGCGA... -
Concatination problem
How can I combine the following inpute sequence as sigle line separated by tab? data_input: >cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 AAGCACCACGAGAAGCUGCAGA >cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 UGAUAUGUCUGGUAUUCUUGGG I have tried: awk '/^>/ {print,"\t"... -
Please awk expert!!!! Filter sequence
I want to filter fastafile using awk. The inpute file looks like Input file: >cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49 AAGCACCACGAGAAGCUGCAGA >cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50 UGAUAUGUCUGGUAUUCUUGGG >cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51... -
More Help, New to awk!!!!
PHV wrote the following script to process the inputfile at the end of this post(it will work for single line process, the problem I have is to extract the last part) awk ' BEGIN{print "loop_beg\tmature_arm\tpri_id"} $1~/^(loop_beg|mature_arm)$/{a[$1]=$2} $1=="pri_id"{print...
