Avishek Kumar avishekrk

For ETS's SKLL project, we found out the hard way that Travis-CI's support for numpy and scipy is pretty abysmal. There are pre-installed versions of numpy for some versions of Python, but those are seriously out of date, and scipy is not there are at all. The two most popular approaches for working around this are to (1) build everything from scratch, or (2) use apt-get to install more recent (but still out of date) versions of numpy and scipy. Both of these approaches lead to longer build times, and with the second approach, you still don't have the most recent versions of anything. To circumvent these issues, we've switched to using Miniconda (Anaconda's lightweight cousin) to install everything.

A template for installing a simple Python package that relies on numpy and scipy using Miniconda is provided below. Since it's a common s

	#!/bin/bash
	mkdir -vp 1fsa_ppsy_i{20,40,60}c1ka5
	ls -F \| grep "^1fsa.*/$" \| while read f;
	do
	f3=$(echo $f\| cut -d_ -f3);
	num=${f3:1:2};
	echo $num;
	fname="peturbed_${num}_input_xxx.pdb";
	echo $fname;
	cd $f;

	#!/bin/bash

	DEST="[email protected]:~/DFI"
	SRCs="/home1/02672/avishek/scratch/InterfacesProject/1fsa/1fsa "

	bckup(){
	rsync -avz -i -h --log-file=$(basename $1)_bckup.txt ${1} ${DEST}
	}

	for src in ${SRCs}; do bckup ${src}; done

	#!/bin/bash

	for d in $(ls -F \| grep "^[a-z].*/$");
	do
	echo $d;
	printf "=========================\n";
	printf "Find covariance matrices\n";
	nm=$(echo $d \| cut -d/ -f1)
	fdfi=$(grep -E "^${nm}:" catalytic_residues.txt \| awk -F: '{print $2}');
	cd $d;

	def fivens_cols(parm):
	sort = {}
	fivens_cols = []
	for col in fivedfi_dict['pctdfi'].columns:
	if 'md' in col:
	continue
	if 'ENM' in col:
	continue
	start, end = col.split('_')
	start = int(start)

	#!/bin/bash
	##run cpptraj for cases where
	##there are not covariance matrics

	module load amber/14

	for f in *.cpptraj;
	do
	echo ${f}
	prefix=$(echo $f \| cut -d. -f1);

	def get_ranges(ranges,delta):
	"""
	Get a range of numberical values
	ranges: ls or numpy array
	delta: sort out range of a certain interval
	"""
	for col in ranges:
	if not('_' in col):
	continue
	start, end = col.split('_')

	def calculate_dfi_windows(pdbid):
	covarmat = glob.glob(pdbid+'_[3-5]?00_????_mwcovarmat.dat')
	pdbfile = pdbid+'.pdb'
	fdfi_residues = ['A235','A340']
	prefix = map(lambda x: x.replace('_mwcovarmat.dat','-dfianalysis.csv'),covarmat)
	for mat, pre in zip(covarmat, prefix):
	print mat, pre
	dfi.calc_dfi(pdbfile,mdhess=mat,ls_reschain=fdfi_residues,writetofile=True,dfianalfile=pre)

	def get_seq(ATOMS):
	from dfi.fafsaseq import mapres
	return ''.join([mapres[i.res_name] for i in ATOMS])

	import pylab as pl
	import numpy as np
	pl.rcParams.update({'font.size': 22})
	a = np.array([[-0.5,1.75]])
	pl.figure(figsize=(4.0, 16))
	img = pl.imshow(a,cmap="seismic")
	pl.gca().set_visible(False)
	#cax = pl.axes([0.1, 0.2, 0.8, 0.6])
	cax= pl.axes([0.35,0.1,0.25,.95])
	pl.colorbar(cax=cax,orientation='vertical')