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ape's Introduction

Ape repository

This repo has scripts used to make chigor.raf, a file in Legofit's .raf format, which contains the chimpanzee and gorilla reference sequences. The repo doesn't contain the data; just the scripts used to generate the data.

The scripts used to download the original data are in subdirectories panTro5 and gorGor5. See the README.md files there for details.

Make .raf file for common chimp reference sequence

sbatch chimpraf.slr

Make .raf file for gorilla reference sequence

sbatch gorraf.slr

Make .raf file for combined chimpanzee and gorilla

sbatch chigor.slr

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ape's Issues

chimpraf.slr fails with error

Hello,

I've managed to download the data, but when I try to convert them to raf using your script, it fails with the following error:

[koci@head ape]$ bash -x chimpraf.slr 
+ export LC_ALL=C
+ LC_ALL=C
+ fmt='panTro5/chr%d.hg19.panTro5.net.axt.gz\n'
+ seq 22
+ sort
+ xargs printf 'panTro5/chr%d.hg19.panTro5.net.axt.gz\n'
+ xargs zcat
+ axt2raf.py
+ sed 's/^chr//'
+ gzip -c
gzip: compressed data not written to a terminal. Use -f to force compression.
For help, type: gzip -h
Traceback (most recent call last):
  File "/home/users/koci/bin/axt2raf.py", line 281, in <module>
    a.pr()
  File "/home/users/koci/bin/axt2raf.py", line 176, in pr
    self.alt[i], self.raf[i])
IOError: [Errno 32] Broken pipe
xargs: zcat: terminated by signal 13

The same error occurs with the gorilla variant of the script. I'm not that good in python to figure out what's wrong. 😕

The axt2raf.py script is in python2, right? It's not obvious from the shebang (#!/usr/bin/python) but on our cluster this points to python2. Running it with python3 gives syntax error.

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