1. Shell Programming and Scripting

My file looks like this: But I would like to 'trim' all sequences to the same lenght 32 characters, keeping intact all the identifier (>GHXCZCC01AJ8CJ) Would it be possible to use awk to perform this task? (2 Replies)

2. Shell Programming and Scripting

My files look like this And I need to cut the sequences at the last "A" found in the following 'pattern' -highlighted for easier identification, the pattern is the actual file is not highlighted. The expected result should look like this Thus, all the sequences would end with AGCCCTA... (2 Replies)

3. Shell Programming and Scripting

This is what I would like to accomplish, I have an input file (file A) that consist of thousands of sequence elements with the same number of characters (length), each headed by a free text header starting with the chevron ‘>' character followed by the ID (all different IDs with different lenghts)... (9 Replies)

4. Shell Programming and Scripting

I got two files right now, input file (target file), reference file 1 (query file) reference file 1 (long list of data) KOLOPWMOPOPO ADASDASD ADSASDASDAD . . target file (one long liner content) ADASDASDTYUKOKOLOPWMOPOPOOPLUAADSASDASDADPOPOUYADADASDASD desired output file content ... (1 Reply)

5. UNIX for Dummies Questions & Answers

Hi, I have a string say "whateverCluster". I need everthing apart from the string "Cluster" Input: whateverCluster Desired output: whatever (5 Replies)

6. Shell Programming and Scripting

Hi, I have a file with more than 28000 records and it looks like below.. >mm10_refflat_ABCD range=chr1:1234567-2345678 tgtgcacactacacatgactagtacatgactagac....so on >mm10_refflat_BCD range=chr1:3234567-4545678... tgtgcacactacacatgactagtatgtgcacactacacatgactagta . . . . . so on ... (2 Replies)

7. Shell Programming and Scripting

I have two files with thousands of sequences of different lengths. infile1 contains the actual sequences and infile2 the scores for each A, T, G and C in infile1. Something like this: infile1: >HZVJKYI01ECH5R TTGATGTGCCAGCTGCCGTTGGTGTGCCAA >HZVJKYI01AQWJ8 GGATATGATGATGAACTGGTTTGGCACACC... (4 Replies)

8. Shell Programming and Scripting

I have to remove sequences from a file based on the distance value. I am attaching the file containing the distances (Distance.xls) The second file looks something like this: Sequences.txt >Sample1 Freq 59 ggatatgatgatgaactggt >Sample1 Freq 54 ggatatgatgttgaactggt >Sample1 Freq 44... (2 Replies)

9. Shell Programming and Scripting

I have a list of IDs in file1 and a list of sequences in file2. I can print sequences from file2, but I'm asking for help in printing the sequences in the same order as the IDs appear in file1. file1: EN_comp12952_c0_seq3:367-1668 ES_comp17168_c1_seq6:1-864 EN_comp13395_c3_seq14:231-1088... (5 Replies)

10. Shell Programming and Scripting

I have this file: >ID1 AA >ID2 TTTTTT >ID-3 AAAAAAAAA >ID4 TTTTTTGGAGATCAGTAGCAGATGACAG-GGGGG-TGCACCCC Add I am trying to use this script to output sequences longer than 15 characters: sed -r '/^>/N;{/^.{,15}$/d}' The desire output would be this: >ID4... (8 Replies)