svn commit: r562414 - in head/biology/haplohseq: . files
Jason W. Bacon
jwb at FreeBSD.org
Sat Jan 23 19:31:51 UTC 2021
Author: jwb
Date: Sat Jan 23 19:31:49 2021
New Revision: 562414
URL: https://svnweb.freebsd.org/changeset/ports/562414
Log:
biology/haplohseq: Fix example scripts for python 3
Also clean up plist
Deleted:
head/biology/haplohseq/files/patch-example_example__run.sh
Modified:
head/biology/haplohseq/Makefile
head/biology/haplohseq/distinfo
head/biology/haplohseq/files/patch-scripts_ldmap.py
head/biology/haplohseq/files/patch-scripts_simple__phaser.py
head/biology/haplohseq/pkg-plist
Modified: head/biology/haplohseq/Makefile
==============================================================================
--- head/biology/haplohseq/Makefile Sat Jan 23 19:30:35 2021 (r562413)
+++ head/biology/haplohseq/Makefile Sat Jan 23 19:31:49 2021 (r562414)
@@ -2,7 +2,7 @@
PORTNAME= haplohseq
DISTVERSION= 0.1.2
-PORTREVISION= 2
+PORTREVISION= 3
CATEGORIES= biology
MAINTAINER= jwb at FreeBSD.org
@@ -26,9 +26,16 @@ MAKE_ENV= STRIP=${STRIP}
SUB_FILES= haplohseq-example
+pre-configure:
+ @${REINPLACE_CMD} \
+ -e 's|/bin/bash|/bin/sh|' \
+ -e 's|python|mkdir example_output; ${PYTHON_CMD}|' \
+ -e 's|\.\./haplohseq|haplohseq|' \
+ ${WRKSRC}/example/example_run.sh
+
post-install-EXAMPLES-on:
${INSTALL_SCRIPT} ${WRKDIR}/haplohseq-example ${STAGEDIR}${PREFIX}/bin
- (cd ${WRKSRC} && ${COPYTREE_SHARE} "example ldmap scripts" ${STAGEDIR}${EXAMPLESDIR})
+ (cd ${WRKSRC} && ${RM} example/*.orig scripts/*.orig && ${COPYTREE_SHARE} "example ldmap scripts" ${STAGEDIR}${EXAMPLESDIR})
do-test:
@(cd ${WRKSRC}/build/test && ${FILESDIR}/run-tests)
Modified: head/biology/haplohseq/distinfo
==============================================================================
--- head/biology/haplohseq/distinfo Sat Jan 23 19:30:35 2021 (r562413)
+++ head/biology/haplohseq/distinfo Sat Jan 23 19:31:49 2021 (r562414)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1589733633
+TIMESTAMP = 1611421648
SHA256 (outpaddling-haplohseq-0.1.2_GH0.tar.gz) = 64f61023a6795decb680c23d142b1a349988d4c0e3bef8c7d52ca33bf42f29f0
SIZE (outpaddling-haplohseq-0.1.2_GH0.tar.gz) = 12084603
Modified: head/biology/haplohseq/files/patch-scripts_ldmap.py
==============================================================================
--- head/biology/haplohseq/files/patch-scripts_ldmap.py Sat Jan 23 19:30:35 2021 (r562413)
+++ head/biology/haplohseq/files/patch-scripts_ldmap.py Sat Jan 23 19:31:49 2021 (r562414)
@@ -1,8 +1,42 @@
---- scripts/ldmap.py.orig 2019-11-13 15:51:02 UTC
+--- scripts/ldmap.py.orig 2021-01-23 17:32:15 UTC
+++ scripts/ldmap.py
-@@ -1,3 +1,5 @@
-+#!/usr/bin/env python2.7
-+
- import argparse
- import sys
- import random
+@@ -29,10 +29,10 @@ class MapMaker:
+ coordinates of the haplotype marker genomic positions.
+ '''
+ def __init__(self, markerFilename, haplotypesFilename):
+- print "reading haplotype base coordinates ...."
++ print("reading haplotype base coordinates ....")
+ self.coords, self.coordIndexes, self.refs, self.alts = self.readMarkers(markerFilename)
+ # self.haplotypes = self.readHaplotypes(haplotypesFilename)
+- print "reading haplotype panel ...."
++ print("reading haplotype panel ....")
+ self.markerCalls = self.readHaplotypes(haplotypesFilename, transpose = True)
+
+ # reads from a vcf file of defined positions representing the haplotype data
+@@ -118,7 +118,7 @@ class MapMaker:
+ # 1) COLLECT MARGINALS AND IDENTIFY SITES THAT ARE POLYMORPHIC
+ # If a site has only one allele in the haplotype panel it is not informative, so it won't be used
+ # in LD calculations. We may want to consider setting some minimum threshold for a minor allele frequency.
+- print "collecting marginal allele counts and identifying polymorphic sites from haplotype panel ...."
++ print("collecting marginal allele counts and identifying polymorphic sites from haplotype panel ....")
+ for index in range(0,len(self.markerCalls)):
+ ref = self.refs[index]
+ alt = self.alts[index]
+@@ -152,7 +152,7 @@ class MapMaker:
+ log.write("Num non-polymorphic sites: " + str(numNonpolymorphicSites) + "\n")
+
+ # 2) CALCULATE D FOR POLYMORPHIC SITES COMPARED WITH N SITES TO THE RIGHT THAT ARE POLYMORPHIC
+- print "calculating D between polymorphic sites and their neighbors ...."
++ print("calculating D between polymorphic sites and their neighbors ....")
+ dVals = []
+ for i in range(0, len(polymorphicIndexes)): # the last coordinate won't have any partners
+ index_i = polymorphicIndexes[i]
+@@ -244,7 +244,7 @@ class LDMap:
+ return ldMap
+
+ def save(self, filename):
+- print "saving ldmap to " + filename
++ print("saving ldmap to " + filename)
+ ldMapFile = open(filename, 'w')
+ ldMapFile.write("\t".join(["COORD","REF","ALT","PAIRED_ALLELES"]) + "\n")
+ for i in range(0,len(self.coords)):
Modified: head/biology/haplohseq/files/patch-scripts_simple__phaser.py
==============================================================================
--- head/biology/haplohseq/files/patch-scripts_simple__phaser.py Sat Jan 23 19:30:35 2021 (r562413)
+++ head/biology/haplohseq/files/patch-scripts_simple__phaser.py Sat Jan 23 19:31:49 2021 (r562414)
@@ -1,8 +1,31 @@
---- scripts/simple_phaser.py.orig 2019-11-13 15:52:02 UTC
+--- scripts/simple_phaser.py.orig 2021-01-23 17:25:56 UTC
+++ scripts/simple_phaser.py
-@@ -1,3 +1,5 @@
-+#!/usr/bin/env python2.7
-+
- import argparse
- import random
- import sys
+@@ -108,7 +108,7 @@ class SimplePhaser:
+ return informativeHets, informativeCoords, informativeIndexes
+
+ def getRefPairedAllele(self, anchorIndex, pairedIndex):
+-# print "\t".join([str(anchorIndex), str(pairedIndex - anchorIndex - 1), str(len(self.ldMap.dVals)),str(len(self.ldMap.dVals[anchorIndex]))]) # prints intermarker counts
++# print("\t".join([str(anchorIndex), str(pairedIndex - anchorIndex - 1), str(len(self.ldMap.dVals)),str(len(self.ldMap.dVals[anchorIndex]))]) # prints intermarker counts)
+ if (pairedIndex - anchorIndex - 1) >= len(self.ldMap.dVals[anchorIndex]):
+ pRef = random.uniform(0,1)
+ if pRef > 0.5:
+@@ -166,8 +166,8 @@ class SimplePhaser:
+ altHap = temp
+
+ if pairedAllele not in [ref,alt]:
+- print "pairedAllele not ref or alt " + ref + " " + alt
+- print pairedAllele
++ print("pairedAllele not ref or alt " + ref + " " + alt)
++ print(pairedAllele)
+
+ return phasedAlleles, informativeCoords
+
+@@ -182,7 +182,7 @@ class SimplePhaser:
+ elif candidateHap[i].upper() == phasedHaps[1][i].upper():
+ currentMatch = 1
+ else:
+- print "ERROR: " + candidateHap[i] + " does not match " + phasedHaps[0][i] + " or " + phasedHaps[1][i] + "\t" + self.ldMap.coords[i] + "\t" + self.ldMap.refs[i] + "\t" + self.ldMap.alts[i]
++ print("ERROR: " + candidateHap[i] + " does not match " + phasedHaps[0][i] + " or " + phasedHaps[1][i] + "\t" + self.ldMap.coords[i] + "\t" + self.ldMap.refs[i] + "\t" + self.ldMap.alts[i])
+ # # randomly assign match
+ # p0 = random.uniform(0,1)
+ # if p0 > 0.5:
Modified: head/biology/haplohseq/pkg-plist
==============================================================================
--- head/biology/haplohseq/pkg-plist Sat Jan 23 19:30:35 2021 (r562413)
+++ head/biology/haplohseq/pkg-plist Sat Jan 23 19:31:49 2021 (r562414)
@@ -5,6 +5,4 @@ bin/haplohseq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ldmap/hg19.exome.ldmap
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scripts/haplohseq_plot.R
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scripts/ldmap.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scripts/ldmap.py.orig
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scripts/simple_phaser.py
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scripts/simple_phaser.py.orig
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