1. Shell Programming and Scripting

Hi.. I have a seperate chromosome sequences and i wanted to parse some regions of chromosome based on start site and end site.. how can i achieve this? For Example Chr 1 is in following format I need regions from 2 - 10 should give me AATTCCAAA and in a similar way 15- 25 should give... (8 Replies)

2. Shell Programming and Scripting

Hi, I have 3 kind of files that contains date data needed to be masked. The file is like this: File 1 (all contents in 1 line): input:DTM+7:201103281411:203'LOC+175+SGSIN:139:6+TERMINATOR......'DTM+132:201103281413:203'LOC.... output:... (4 Replies)

3. Shell Programming and Scripting

Hello guys, I guess you are fed up with sed command and parse questions, but after a while researching the forum, I could not get an answer to my doubt. I know it must be easy done with sed command, but unfortunately, I never get right syntax of this command OK, this is what I have in my... (3 Replies)

4. UNIX for Dummies Questions & Answers

Hi I have an alignment file (.fasta) with ~80 sequences. They look like this- >JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0 GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)

5. UNIX for Dummies Questions & Answers

Hi, I have a file1 of many long sequences, each preceded by a unique header line. file2 is 3-columns list: headers name, start position, end position. I'd like to extract the sequence region of file1 specified in file2. Based on a post elsewhere, I found the code: awk... (2 Replies)

6. Shell Programming and Scripting

Hi, I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help . input > fefrwefrwef X900 AGAGGGAATTGG AGGGGCCTGGAG GGTTCTCTTC > fefrwefrwef X932 AGAGGGAATTGG AGGAGGTGGAG GGTTCTCTTC > fefrwefrwef X937... (2 Replies)

7. Shell Programming and Scripting

I would like to take a fasta file formated like >0001 agttcgaggtcagaatt >0002 agttcgag >0003 ggtaacctga and use command line perl to move the all sample gt 8 in length to a new file. the result would be >0001 agttcgaggtcagaatt >0003 ggtaacctga cat ${sample}.fasta | perl -lane... (2 Replies)

8. Shell Programming and Scripting

Hello, here I am posting my query again with modified data input files. see my query is : i have two input files file1 and file2. file1 is smalldata.fasta >gi|546671471|gb|AWWX01449637.1| Bubalus bubalis breed Mediterranean WGS:AWWX01:contig449636, whole genome shotgun sequence... (20 Replies)

9. UNIX for Dummies Questions & Answers

I have the following script: awk 'FNR==NR{s+=$3;next;} { print $1 , $2, 100*$3/s }' and the following file: >P39PT-1224 Freq 900 cccctacgacggcattggtaatggctcagctgctccggatcccgcaagccatcttggatatgagggttcgtcggcctcttcagccaagg-cccccagcagaacatccagctgatcg >P39PT-784 Freq 2... (2 Replies)

10. Shell Programming and Scripting

Input File: >Seq1 ASDADAFASFASFADGSDGFSDFSDFSDFSDFSDFSDFSDFSDFSDFSDFSD >Seq2 SDASDAQEQWEQeqAdfaasd >Seq3 ASDSALGHIUDFJANCAGPATHLACJHPAUTYNJKG ...... Desired Output File >Seq1 ASDADAFASF ASFADGSDGF SDFSDFSDFS DFSDFSDFSD FSDFSDFSDF SD >Seq2 (4 Replies)