I have a data in that always comes in block of four in the following format (called FASTQ): @SRR018006.2016 GA2:6:1:20:650 length=36 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGN +SRR018006.2016 GA2:6:1:20...

I need to make a list of a large number of files (40,000 files) like below: ERR001268_1_100.fastq ERR001268_2_156.fastq ERR001753_2_78.fastq ERR001268_1_101.fastq ERR001268_2_157.fastq ERR001753_2...

I'm pretty new to Python, and I have written a (probably very ugly) script that is supposed to randomly select a subset of sequences from a fastq-file. A fastq-file stores information in blocks of ...

I have following task: Starting with 30 character long pattern sequence (it is actually DNA sequence, lest call it P30) I need to find in a text file all lines starting (^agacatacag... )with a exac...

This is my script: #!/bin/bash #script to loop through directories to merge fastq files sourcedir=/path/to/source destdir=/path/to/dest for f in $sourcedir/* do fbase=$(basename "$f") echo "In...

I am pretty new at shell scripting and I have been struggling all day to figure out how to perform a "for" command. Essentially, what I am trying to do is the following: I have a list.txt file wit...

I have to check presence of millions of elements (20-30 letters str) in the list containing 10-100k of those elements. Is there faster way of doing that in python than set() ? import sys #load ids...

Background: Python 2.6.6 on Linux. First part of a DNA sequence analysis pipeline. I want to read a possibly gzipped file from a mounted remote storage (LAN) and if it is gzipped; gunzip it to a st...