Terms in Pseudopipe output, etc

Q:
I am looking the details of Pseudopipe’s output terms such as "frac", "ins", "del", "shift", "stop", "polya". Also how pseudopipe makes confirm the pseudogenes in its results.

A:
frac = fraction of parent gene that matches the pseudogene
ins = number of insertions in the pseudogene compared to parent sequence
del = number of deletions in the pseudogene compared to parent sequence
shift = number of frame shifts in the pseudogene compared to parent sequence
stop = number of stop codons in the pseudogene compared to parent sequence
polya = flag indicating the presence or absence of a polyA tail

Also see below the code associated with the script fetchEnsemblFiles.py for downloading the input data for eukaryotes from ensembl website:


#!/usr/bin/env python

# some examples of files and locations
# pub
# lrwxrwxrwx 1 ftpuser ftpusers 30 Dec 7 16:33 current_homo_sapiens -> release-36/homo_sapiens_36_35i
#
#/pub/release-36/homo_sapiens_36_35i/data/fasta/dna
#-rw-rw-r– 1 ftpuser ftpusers 67675771 Nov 15 14:48 Homo_sapiens.NCBI35.dec.dna.chromosome.1.fa.gz
#-rw-rw-r– 1 ftpuser ftpusers 40802343 Nov 15 14:55 Homo_sapiens.NCBI35.dec.dna_rm.chromosome.1.fa.gz
#
#/pub/release-36/homo_sapiens_36_35i/data/fasta/pep
#-rw-rw-r– 1 ftpuser ftpusers 3817861 Nov 15 19:46 Homo_sapiens.NCBI35.dec.pep.known.fa.gz
#
#/pub/release-36/homo_sapiens_36_35i/data/mysql/homo_sapiens_core_36_35i
#-rw-rw-r– 1 ftpuser ftpusers 2957452 Dec 2 22:45 exon.txt.table.gz
#-rw-rw-r– 1 ftpuser ftpusers 1747738 Dec 2 22:45 exon_stable_id.txt.table.gz
#-rw-rw-r– 1 ftpuser ftpusers 1489045 Dec 2 22:45 exon_transcript.txt.table.gz
#-rw-rw-r– 1 ftpuser ftpusers 4626 Dec 2 21:57 homo_sapiens_core_36_35i.mysql40_compatible.sql.gz
#-rw-rw-r– 1 ftpuser ftpusers 4753 Dec 2 21:57 homo_sapiens_core_36_35i.sql.gz

import os, os.path, re, sys
from ftplib import FTP

class collect:
def __init__(self): self.data = []
def more(self, l): self.data.append(l)

def maybeRetrFile(fromPath, toPath):
what = ‘from %s –> to %s’ %(fromPath, toPath)
if os.path.exists(toPath):
print ‘skipping ‘+what
return
else:
if toPath.endswith(‘.gz’) and os.path.exists(toPath[:-3]):
print ‘skipping (uncompressed) ‘+what
return

print what
toFile = open(toPath, ‘w’)
ec.retrbinary(‘RETR ‘+fromPath, toFile.write, blocksize=100000)
toFile.close()

target = sys.argv[1].strip().lower().replace(‘ ‘, ‘_’)

release = ‘current_’

if len(sys.argv) > 2:
release = ‘release-‘ + sys.argv[2] + ‘/’

# set up initial connection
host=’ftp.ensemblgenomes.org’
print ‘Logging into ‘+host
ec = FTP(host)
ec.login()

# look for target in a listing of pub
files = collect()
where=’pub/’+release+’mysql’
print ‘Listing ‘+where
ec.dir(where, files.more)
tEntries = [l for l in files.data if target+”_core_” in l and ‘->’ not in l ]
if len(tEntries) != 1:
print target + ‘ is either missing or not unique:’
print tEntries
print ‘\n’.join(files.data)
ec.close()
sys.exit(-1)

# “parse” current link name
curPat = re.compile(r”+target+’_core_(.+)_(.+)\Z’)
tPath = tEntries[0].split()[-1]
mo = curPat.match(tPath)
if not mo:
print ‘dont\’t understand release naming scheme: ‘+ tPath
ec.close()
sys.exit(-1)
[maj, min] = mo.groups()
majMin=maj+’_’+min
outDir = target + ‘_’ + majMin

print ‘Release: ‘+release[0:len(release)-1]+’, ‘+’tPath: ‘+tPath+’, ‘+’target: ‘+target+’, ‘+’maj: ‘+maj+’, ‘+’majMin: ‘+majMin+’, ‘+’outDir: ‘+outDir

## if os.path.exists(outDir):
## print ‘up to date: ‘ + tPath
## ec.close()
## sys.exit(0)

# need to get files. first, set up directories.
[dDir, mDir, pDir] = [outDir+d for d in [‘/dna/’, ‘/mysql/’, ‘/pep/’]]
if not os.path.exists(dDir): os.makedirs(dDir, 0744)
if not os.path.exists(mDir): os.makedirs(mDir, 0744)
if not os.path.exists(pDir): os.makedirs(pDir, 0744)

# retrieve dna
dnaPat = re.compile(r’\.dna(_rm)?\.chromosome\..+\.fa\.gz\Z’)
dFiles = collect()
where = ‘pub/’+release+’fasta/%s/dna’ % target
print ‘Changing dir to ‘+where
ec.dir(where, dFiles.more)
dKeep = [l for l in dFiles.data if dnaPat.search(l)]
for f in dKeep:
fn = f.split()[-1]
maybeRetrFile(where+’/’+fn, dDir+fn)

# retrieve pep
where = ‘pub/’+release+’fasta/%s/pep’ % target
pFiles = collect()
print ‘Changing dir to ‘+where
ec.dir(where, pFiles.more)
for f in pFiles.data:
fn = f.split()[-1]
maybeRetrFile(where+’/’+fn, pDir+fn)

# retrieve mysql
# older releases?: mFiles = [‘exon.txt.table’, ‘exon_transcript.txt.table’, ‘gene_stable_id.txt.table’, ‘seq_region.txt.table’, ‘transcript.txt.table’, ‘translation.txt.table’, ‘translation_stable_id.txt.table’, target+’_core_’+majMin+’.sql’, target+’_core_’+majMin+’.mysql40_compatible.sql’]
#older releases which have *_stable_id.txt: mFiles = [‘exon.txt’, ‘exon_transcript.txt’, ‘gene_stable_id.txt’, ‘seq_region.txt’, ‘transcript.txt’, ‘translation.txt’, ‘translation_stable_id.txt’, target+’_core_’+majMin+’.sql’]
mFiles = [‘exon.txt’, ‘exon_transcript.txt’, ‘seq_region.txt’, ‘transcript.txt’, ‘translation.txt’, target+’_core_’+majMin+’.sql’]

where = ‘pub/’+release+’mysql/%s_core_%s’ % (target, majMin)
print ‘Changing dir to ‘+where
for mf in mFiles:
maybeRetrFile(where+’/’+mf+’.gz’, mDir+mf+’.gz’)

# retrieve GTF
where = ‘pub/’+release+’gtf/%s’ % (target)
print ‘Changing dir to ‘+where
gtfPat = re.compile(r’\.gtf\.gz\Z’)
gFiles = collect()
ec.dir(where, gFiles.more)
gKeep = [l for l in gFiles.data if gtfPat.search(l)]
for f in gKeep:
fn = f.split()[-1]
maybeRetrFile(where+’/’+fn, mDir+fn)

ec.close()

print ‘Processing Fetched Files’
#os.system(‘%s/processEnsemblFiles.sh %s’ % (sys.path[0], outDir))

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