[SOLVED] Separating interleaved lines into two different files

Lokelo · 11-28-2011, 02:34 AM

After managing to solve a few minor programming issues on my own (I assume in a rather crude way, but they work) I got stuck with another problem I'm not really sure how to solve.

I have a file with interleaved data:

Code:

@HWI-ST261:396:I0D48ABXX:8:1101:1354:2103/1
ATCCGATTGGATTAACATAGTGCTACACTTAATAGATGCCGTTGGCCTCCTCCCAACGAGACTTGACTTTAGTCT
+
HHJJJIJJIJIJJJJJIJIJIIJJIJJJJJIGIIIIIJJJJIIGGHIJJJJIHGIJHHFFEFEECEEDDDDDDDE
@HWI-ST261:396:I0D48ABXX:8:1101:1354:2103/2
CCTCGCGCGTGTGCCTTTCTGGAACGGCAAAGATTCGGAAGCGATGAAGAACGCGGAAAGGACCAAGGAGATGAT
+
HHJJJJJJJHHHIJIJJJJJJJIIHHIJJJJJJJJIHHHHFFDDDDDCDDDD=BBBDD>ABDDDDDDDBB?>@C@
@HWI-ST261:396:I0D48ABXX:8:1101:1536:2081/1
CTCCACCCACCCGATCGTGCAGCACAACTCTTACACTGCCTGGTTTGCAGAGGGAGAGGCAAGCGAGGCGCAGCT
+
HHJIJJJJJJJJJIJJHBGHIJJJJIHGIIIIJIIGEHHHGEF@DFCEEECDBBBB?B@BDD????<@><5<<@A
@HWI-ST261:396:I0D48ABXX:8:1101:1536:2081/2
GTGCGAGGAGGAAGACATTGGAGAAGACGGAGAACTGCACGACGAGCTCCCTCAGCTGCGCCTCGCTTGCCTCTC
+
HFHIJGIJEIJGGHEHIJJJJIJIGIJIHJJIIAFHIJJHIJHHFDBDDDDDD?CD>CDDB@>BDD<ABBCCCCC
@HWI-ST261:396:I0D48ABXX:8:1101:1721:2085/1
CCAGCGACATTTTCGAACGTTACTGGGTCGTTCTTCACATCTCGTGGACCATCAAATGGCTCCATGGAGCAATCG
+
HHGHGHGIIIHIIIGIIIIHIGIIIIIGHIII@GGAC==@CGGCCAEDDF<@C;>;;>CDDDBCC(>@AA(5>CB
@HWI-ST261:396:I0D48ABXX:8:1101:1721:2085/2
GCTCGAGCACCATGTGGACATCGTCAAGCTGAAGGACTGCCAGTGCGACTTGCAGCCAGAGTTTGTCGATTGCTC
+
HHJJIJIGIJJCHIIIIIJGGHHCGIIJJGHHIJGIIJIDHHIIIIIJIFHFHDDB?>@BC6>CDDD8?8>7:55
@HWI-ST261:396:I0D48ABXX:8:1101:1861:2094/1
GCCTCGCTCGCCTTCTTGCGAACCACCTTCTTCCCATCATTGCTATCACCACTATTGCCATCCTTCGAGTCCTTC
+
HHJIJJGIJJJJJJIGIJGIJIEIIIIIIIIIHHIJIFHFHHHEEECCEC@CECCDDDDDCDDDDCABC>CCDDC
@HWI-ST261:396:I0D48ABXX:8:1101:1861:2094/2
CGAACTTGTTCGATGACAATCAGACATTCGCCGGCTCTTTCATGCCCATCTTTGGTAAGGGTGACCCGATCATTA
+
HHGIIIIIHJJJGGJJJJJJJJJIJJIJJJJHHGHEGHIHIGJJHHHHHFFFFFFDC>AC?=BBDDDDDBBB>@A

The lines starting with @HWI are the ID of the data in the next 3 lines, so every 4 lines are one data entry.

I would like to have all the data of the ID's ending in /1 in one file and with /2 in another file and they need to be in the exact same order.

I know I can pull out single lines with awk and grep, but I'm not sure how I could pull out the following three lines, too.

druuna · 11-28-2011, 03:07 AM

Hi,

Here's a "dirty", but working solution:

Code:

#!/bin/bash

awk '
/^@HWI.*\/1/ { print > "file1"
  getline ; print  > "file1"
  getline ; print  > "file1"
  getline ; print > "file1"
}
/^@HWI.*\/2/ { print > "file2"
  getline ; print  > "file2"
  getline ; print  > "file2"
  getline ; print > "file2"
}
' infile

Hope this helps.

Lokelo · 11-28-2011, 03:26 AM

It seems to work just fine! thanks!

druuna · 11-28-2011, 03:33 AM

You're welcome