Index: head/biology/Makefile
===================================================================
--- head/biology/Makefile	(revision 482398)
+++ head/biology/Makefile	(revision 482399)
@@ -1,147 +1,148 @@
 # $FreeBSD$
 #
 
     COMMENT = Biology
 
     SUBDIR += artemis
     SUBDIR += avida
     SUBDIR += babel
     SUBDIR += bamtools
     SUBDIR += bcftools
     SUBDIR += bedtools
     SUBDIR += biococoa
     SUBDIR += bowtie
     SUBDIR += bowtie2
     SUBDIR += bwa
     SUBDIR += canu
     SUBDIR += cd-hit
     SUBDIR += cdbfasta
     SUBDIR += chemeq
     SUBDIR += clustal-omega
     SUBDIR += clustalw
     SUBDIR += clustalx
     SUBDIR += consed
     SUBDIR += cytoscape
     SUBDIR += ddocent
     SUBDIR += diamond
     SUBDIR += emboss
     SUBDIR += exonerate
     SUBDIR += fasta
     SUBDIR += fasta3
     SUBDIR += fastahack
     SUBDIR += fastdnaml
     SUBDIR += fastool
     SUBDIR += fastqc
     SUBDIR += fasttree
     SUBDIR += fastx-toolkit
     SUBDIR += fluctuate
     SUBDIR += freebayes
     SUBDIR += garlic
     SUBDIR += gff2ps
     SUBDIR += gmap
     SUBDIR += gperiodic
     SUBDIR += grappa
     SUBDIR += hmmer
     SUBDIR += htslib
     SUBDIR += hyphy
     SUBDIR += igv
     SUBDIR += infernal
     SUBDIR += iolib
     SUBDIR += iqtree
     SUBDIR += jalview
     SUBDIR += jellyfish
     SUBDIR += kallisto
     SUBDIR += lagan
     SUBDIR += lamarc
     SUBDIR += libgtextutils
     SUBDIR += libsbml
     SUBDIR += linux-foldingathome
     SUBDIR += mafft
     SUBDIR += mapm3
     SUBDIR += migrate
     SUBDIR += molden
     SUBDIR += mopac
     SUBDIR += mrbayes
     SUBDIR += mummer
     SUBDIR += muscle
     SUBDIR += ncbi-blast+
     SUBDIR += ncbi-cxx-toolkit
     SUBDIR += ncbi-toolkit
     SUBDIR += ngs-sdk
     SUBDIR += njplot
     SUBDIR += p5-AcePerl
     SUBDIR += p5-Bio-ASN1-EntrezGene
     SUBDIR += p5-Bio-Coordinate
     SUBDIR += p5-Bio-Das
     SUBDIR += p5-Bio-Das-Lite
     SUBDIR += p5-Bio-FeatureIO
     SUBDIR += p5-Bio-GFF3
     SUBDIR += p5-Bio-Glite
     SUBDIR += p5-Bio-Graphics
     SUBDIR += p5-Bio-MAGETAB
     SUBDIR += p5-Bio-NEXUS
     SUBDIR += p5-Bio-Phylo
     SUBDIR += p5-Bio-SCF
     SUBDIR += p5-BioPerl
     SUBDIR += p5-BioPerl-Run
     SUBDIR += p5-TrimGalore
     SUBDIR += p5-transdecoder
     SUBDIR += paml
     SUBDIR += pbbam
     SUBDIR += pbcopper
     SUBDIR += pbseqan
     SUBDIR += pear-merger
     SUBDIR += phrap
     SUBDIR += phred
     SUBDIR += phylip
     SUBDIR += phyml
     SUBDIR += plinkseq
     SUBDIR += primer3
     SUBDIR += protomol
     SUBDIR += psi88
     SUBDIR += py-Genesis-PyAPI
     SUBDIR += py-biom-format
     SUBDIR += py-biopython
     SUBDIR += py-bx-python
     SUBDIR += py-cutadapt
     SUBDIR += py-gtfparse
     SUBDIR += py-loompy
     SUBDIR += py-macs2
     SUBDIR += py-orange3-bioinformatics
     SUBDIR += py-orange3-single-cell
+    SUBDIR += py-pyfaidx
     SUBDIR += py-pysam
     SUBDIR += pycogent
     SUBDIR += pyfasta
     SUBDIR += python-nexus
     SUBDIR += rainbow
     SUBDIR += recombine
     SUBDIR += ruby-bio
     SUBDIR += rubygem-bio
     SUBDIR += samtools
     SUBDIR += seaview
     SUBDIR += seqan
     SUBDIR += seqan-apps
     SUBDIR += seqan1
     SUBDIR += seqio
     SUBDIR += seqtk
     SUBDIR += seqtools
     SUBDIR += sim4
     SUBDIR += slclust
     SUBDIR += smithwaterman
     SUBDIR += stacks
     SUBDIR += stringtie
     SUBDIR += tRNAscan-SE
     SUBDIR += t_coffee
     SUBDIR += tabixpp
     SUBDIR += treepuzzle
     SUBDIR += trimadap
     SUBDIR += trimmomatic
     SUBDIR += ugene
     SUBDIR += unanimity
     SUBDIR += vcflib
     SUBDIR += vcftools
     SUBDIR += velvet
     SUBDIR += wise
     SUBDIR += xmolwt
 
 .include <bsd.port.subdir.mk>
Index: head/biology/py-pyfaidx/Makefile
===================================================================
--- head/biology/py-pyfaidx/Makefile	(nonexistent)
+++ head/biology/py-pyfaidx/Makefile	(revision 482399)
@@ -0,0 +1,21 @@
+# $FreeBSD$
+
+PORTNAME=	pyfaidx
+DISTVERSION=	0.5.5.1
+CATEGORIES=	biology python
+MASTER_SITES=	CHEESESHOP
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Efficient pythonic random access to fasta subsequences
+
+LICENSE=	BSD3CLAUSE
+
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR}
+
+USES=		python
+USE_PYTHON=	distutils concurrent autoplist
+
+NO_ARCH=	yes
+
+.include <bsd.port.mk>

Property changes on: head/biology/py-pyfaidx/Makefile
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:keywords
## -0,0 +1 ##
+FreeBSD=%H
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Added: svn:mime-type
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+text/plain
\ No newline at end of property
Index: head/biology/py-pyfaidx/distinfo
===================================================================
--- head/biology/py-pyfaidx/distinfo	(nonexistent)
+++ head/biology/py-pyfaidx/distinfo	(revision 482399)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1539913803
+SHA256 (pyfaidx-0.5.5.1.tar.gz) = d216924c901f39d445e13e574583442cd09f67424e13c2d33a5aacdfd367d39d
+SIZE (pyfaidx-0.5.5.1.tar.gz) = 30205

Property changes on: head/biology/py-pyfaidx/distinfo
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: head/biology/py-pyfaidx/pkg-descr
===================================================================
--- head/biology/py-pyfaidx/pkg-descr	(nonexistent)
+++ head/biology/py-pyfaidx/pkg-descr	(revision 482399)
@@ -0,0 +1,13 @@
+FASTA is a format to exchange generic information, partial or of the entire
+organism.
+
+A function "faidx" (FAsta InDeX) creates a small flat index file ".fai" allowing
+for fast random access to any subsequence in the indexed FASTA file, while
+loading a minimal amount of the file in to memory. This python module implements
+pure Python classes for indexing, retrieval, and in-place modification of FASTA
+files using a samtools compatible index. The pyfaidx module is API compatible
+with the pygr seqdb module. A command-line script "faidx" is installed alongside
+the pyfaidx module, and facilitates complex manipulation of FASTA files without
+any programming knowledge.
+
+WWW: https://github.com/mdshw5/pyfaidx

Property changes on: head/biology/py-pyfaidx/pkg-descr
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property