1. Shell Programming and Scripting

Hi Guru's, I am trying to grep a range of line numbers (based on match) and then look for another match which starts with a special character '$' and print the line number. I have the below code but it is actually printing the line number counting starting from the first line of the range i am... (15 Replies)

2. Shell Programming and Scripting

In the files attached, I am trying to: if Files.txt $1 is in the range of Exons.txt $1, then in Files.txt $4 the value from Exons.txt $3 is copied else if no match is found Exons.txt $3 = "Intron" For example, the first value in File.txt $1 is chr1:14895-14944 and is not found in any range... (4 Replies)

3. Shell Programming and Scripting

Hi All, Seeking for your assistance to print all the specific field when the condition met. Ex: file1.txt 1|203|3|31243|5341|6452|623|22|00|01 3|45345|123214|6534|3423|6565|643|343|232|10 if field 1 = 1 and field 3 = 3 and field 5 = 5341 and field 6 = 6452 it will print from $1 to $10.... (2 Replies)

4. Shell Programming and Scripting

Hello, I have a text file in the below format: Source Destination State Lag Status CQA02W2K12pl:D:\CAQA ... (10 Replies)

5. Shell Programming and Scripting

I am trying to use awk to print the unique entries in $2 So in the example below there are 3 lines but 2 of the lines match in $2 so only one is used in the output. File.txt chr17:29667512-29667673 NF1:exon.1;NF1:exon.2;NF1:exon.38;NF1:exon.4;NF1:exon.46;NF1:exon.47 703.807... (5 Replies)

6. Shell Programming and Scripting

Trying to print the unique values in $2 before the -, currently the count is displayed. Hopefully, the below is close. Thank you :). file chr2:46603668-46603902 EPAS1-902|gc=54.3 253.1 chr2:211471445-211471675 CPS1-1205|gc=48.3 264.7 chr19:15291762-15291983 NOTCH3-1003|gc=68.8 195.8... (3 Replies)

7. Shell Programming and Scripting

In file1 field $18 is removed.... column header is "Otherinfo", then each line in file1 is used to search file2 for a match. When a match is found the last four strings in file2 are copied to file1. Maybe: cut -f1-17 file1 and then match each line to file2 file1 Chr Start End ... (6 Replies)

8. Shell Programming and Scripting

I am trying to use awk to find all the $2 values in file2 which is ~30MB and tab-delimited, that are between $2 and $3 in file1 which is ~2GB and tab-delimited. I have just found out that I need to use $1 and $2 and $3 from file1 and $1 and $2of file2 must match $1 of file1 and be in the range... (6 Replies)

9. UNIX for Beginners Questions & Answers

I have a file.txt containing the following: Query= HWI-ST863:386:C5Y8UACXX:3:2302:16454:89688 1:N:0:ACACGAAT Length=100 Score E Sequences producing significant alignments: (Bits) Value ... (2 Replies)

10. Shell Programming and Scripting

In the awk below I am trying to print the entire line, along with the header row, if $2 is SNV or MNV or INDEL. If that condition is met or is true, and $3 is less than or equal to 0.05, then in $7 the sub pattern :GMAF= is found and the value after the = sign is checked. If that value is less than... (0 Replies)